From 43b79f1bf8bec4461e6dc3bbf185a5894b9891de Mon Sep 17 00:00:00 2001
From: Ceyda Cinarel <snu-ceyda@users.noreply.github.com>
Date: Thu, 21 May 2020 20:49:30 +0900
Subject: [PATCH 1/6] add sudo_options kwarg, add env kwarg to run_command

---
 spython/instance/cmd/start.py | 4 ++--
 spython/main/execute.py       | 5 +++--
 spython/main/instances.py     | 4 ++--
 spython/utils/terminal.py     | 4 +++-
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/spython/instance/cmd/start.py b/spython/instance/cmd/start.py
index f1c5230f..bd4c85b0 100644
--- a/spython/instance/cmd/start.py
+++ b/spython/instance/cmd/start.py
@@ -9,7 +9,7 @@
 
 
 def start(
-    self, image=None, name=None, args=None, sudo=False, options=None, capture=False
+    self, image=None, name=None, args=None, sudo=False, sudo_options=None, options=None, capture=False, env=None
 ):
     """start an instance. This is done by default when an instance is created.
 
@@ -69,7 +69,7 @@ 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, env=env)
 
     if output["return_code"] == 0:
         self._update_metadata()
diff --git a/spython/main/execute.py b/spython/main/execute.py
index 43ad0944..d2dde647 100644
--- a/spython/main/execute.py
+++ b/spython/main/execute.py
@@ -24,6 +24,7 @@ def execute(
     return_result=False,
     options=None,
     sudo=False,
+    sudo_options=None,
     quiet=True,
 ):
     """ execute: send a command to a container
@@ -97,9 +98,9 @@ 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
             )
-        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
index d134cde4..87d3ac0c 100644
--- a/spython/main/instances.py
+++ b/spython/main/instances.py
@@ -9,7 +9,7 @@
 from spython.utils import run_command
 
 
-def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
+def list_instances(self, name=None, return_json=False, quiet=False, sudo=False, sudo_options=None):
     """list instances. For Singularity, this is provided as a command sub
        group.
 
@@ -45,7 +45,7 @@ def list_instances(self, name=None, return_json=False, quiet=False, sudo=False):
     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
index 8ce14613..63c426ab 100644
--- a/spython/utils/terminal.py
+++ b/spython/utils/terminal.py
@@ -151,6 +151,7 @@ def run_command(
     no_newline_regexp="Progess",
     quiet=False,
     sudo_options=None,
+    env=None
 ):
 
     """run_command uses subprocess to send a command to the terminal. If
@@ -176,7 +177,8 @@ 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=env)
     lines = []
     found_match = False
 

From 167c334022d2a02cc95561289d0fbc3e2f90445f Mon Sep 17 00:00:00 2001
From: Ceyda Cinarel <snu-ceyda@users.noreply.github.com>
Date: Fri, 5 Jun 2020 09:09:19 +0900
Subject: [PATCH 2/6] add sudo_options to instance stop

---
 spython/instance/cmd/stop.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/spython/instance/cmd/stop.py b/spython/instance/cmd/stop.py
index 09c0367d..36c9a8a4 100644
--- a/spython/instance/cmd/stop.py
+++ b/spython/instance/cmd/stop.py
@@ -8,7 +8,7 @@
 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 +42,7 @@ 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"])

From d0564b948953aa319a549fbd60908f79726b3dbf Mon Sep 17 00:00:00 2001
From: Ceyda Cinarel <snu-ceyda@users.noreply.github.com>
Date: Mon, 14 Sep 2020 16:02:41 +0900
Subject: [PATCH 3/6] add environment parameter to run_command

---
 spython/main/base/command.py | 3 ++-
 spython/main/execute.py      | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/spython/main/base/command.py b/spython/main/base/command.py
index 36204b09..626d5b16 100644
--- 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,
+    env=None,
 ):
 
     """run_command is a wrapper for the global run_command, checking first
@@ -130,7 +131,7 @@ 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, env=env
     )
 
     # If one line is returned, squash dimension
diff --git a/spython/main/execute.py b/spython/main/execute.py
index f66ecc1c..e005e598 100644
--- a/spython/main/execute.py
+++ b/spython/main/execute.py
@@ -27,6 +27,7 @@ def execute(
     sudo=False,
     sudo_options=None,
     quiet=True,
+    env=None,
 ):
     """ execute: send a command to a container
     
@@ -100,7 +101,7 @@ def execute(
 
         if not stream:
             return self._run_command(
-                cmd, sudo=sudo, sudo_options=sudo_options, return_result=return_result, quiet=quiet
+                cmd, sudo=sudo, sudo_options=sudo_options, return_result=return_result, quiet=quiet, env=env
             )
         return stream_command(cmd, sudo=sudo, sudo_options=sudo_options)
 

From bc7b346b0b9d0bacc258dd7e24a81d58ee99dec9 Mon Sep 17 00:00:00 2001
From: Ceyda Cinarel <snu-ceyda@users.noreply.github.com>
Date: Mon, 14 Sep 2020 16:44:46 +0900
Subject: [PATCH 4/6] lint code

---
 spython/instance/cmd/start.py | 6 ++++--
 spython/instance/cmd/stop.py  | 9 ++++++++-
 spython/main/execute.py       | 7 ++++++-
 spython/utils/terminal.py     | 2 +-
 4 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/spython/instance/cmd/start.py b/spython/instance/cmd/start.py
index 58aeed1b..2f56b0bc 100644
--- a/spython/instance/cmd/start.py
+++ b/spython/instance/cmd/start.py
@@ -18,7 +18,7 @@ def start(
     options=None,
     capture=False,
     singularity_options=None,
-    env=None
+    env=None,
 ):
     """start an instance. This is done by default when an instance is created.
 
@@ -79,7 +79,9 @@ def start(
     self.args = args
     self.cmd = cmd
 
-    output = run_command(cmd, sudo=sudo, sudo_options=sudo_options, quiet=True, capture=capture, env=env)
+    output = run_command(
+        cmd, sudo=sudo, sudo_options=sudo_options, quiet=True, capture=capture, env=env
+    )
 
     if output["return_code"] == 0:
         self._update_metadata()
diff --git a/spython/instance/cmd/stop.py b/spython/instance/cmd/stop.py
index 36c9a8a4..c6017946 100644
--- 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,  sudo_options=None, 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
diff --git a/spython/main/execute.py b/spython/main/execute.py
index e005e598..77981451 100644
--- a/spython/main/execute.py
+++ b/spython/main/execute.py
@@ -101,7 +101,12 @@ def execute(
 
         if not stream:
             return self._run_command(
-                cmd, sudo=sudo, sudo_options=sudo_options, return_result=return_result, quiet=quiet, env=env
+                cmd,
+                sudo=sudo,
+                sudo_options=sudo_options,
+                return_result=return_result,
+                quiet=quiet,
+                env=env,
             )
         return stream_command(cmd, sudo=sudo, sudo_options=sudo_options)
 
diff --git a/spython/utils/terminal.py b/spython/utils/terminal.py
index b36d04ce..b844d9b7 100644
--- a/spython/utils/terminal.py
+++ b/spython/utils/terminal.py
@@ -154,7 +154,7 @@ def run_command(
     no_newline_regexp="Progess",
     quiet=False,
     sudo_options=None,
-    env=None
+    env=None,
 ):
 
     """run_command uses subprocess to send a command to the terminal. If

From c72c4932e125df826922f3956c18e7c6e4144e95 Mon Sep 17 00:00:00 2001
From: Ceyda Cinarel <snu-ceyda@users.noreply.github.com>
Date: Tue, 15 Sep 2020 18:12:10 +0900
Subject: [PATCH 5/6] rename env to environ

---
 CHANGELOG.md                  | 2 ++
 spython/instance/cmd/start.py | 4 ++--
 spython/main/base/command.py  | 4 ++--
 spython/main/execute.py       | 4 ++--
 spython/utils/terminal.py     | 4 ++--
 spython/version.py            | 2 +-
 6 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 91fbad0e..bbf4922d 100644
--- 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
index 2f56b0bc..e9ad9c69 100644
--- a/spython/instance/cmd/start.py
+++ b/spython/instance/cmd/start.py
@@ -18,7 +18,7 @@ def start(
     options=None,
     capture=False,
     singularity_options=None,
-    env=None,
+    environ=None,
 ):
     """start an instance. This is done by default when an instance is created.
 
@@ -80,7 +80,7 @@ def start(
     self.cmd = cmd
 
     output = run_command(
-        cmd, sudo=sudo, sudo_options=sudo_options, quiet=True, capture=capture, env=env
+        cmd, sudo=sudo, sudo_options=sudo_options, quiet=True, capture=capture, environ=environ
     )
 
     if output["return_code"] == 0:
diff --git a/spython/main/base/command.py b/spython/main/base/command.py
index 626d5b16..bc352021 100644
--- a/spython/main/base/command.py
+++ b/spython/main/base/command.py
@@ -108,7 +108,7 @@ def run_command(
     quiet=None,
     return_result=False,
     sudo_options=None,
-    env=None,
+    environ=None,
 ):
 
     """run_command is a wrapper for the global run_command, checking first
@@ -131,7 +131,7 @@ def run_command(
         quiet = self.quiet
 
     result = run_cmd(
-        cmd, sudo=sudo, capture=capture, quiet=quiet, sudo_options=sudo_options, env=env
+        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
index 77981451..62d127bb 100644
--- a/spython/main/execute.py
+++ b/spython/main/execute.py
@@ -27,7 +27,7 @@ def execute(
     sudo=False,
     sudo_options=None,
     quiet=True,
-    env=None,
+    environ=None,
 ):
     """ execute: send a command to a container
     
@@ -106,7 +106,7 @@ def execute(
                 sudo_options=sudo_options,
                 return_result=return_result,
                 quiet=quiet,
-                env=env,
+                environ=environ,
             )
         return stream_command(cmd, sudo=sudo, sudo_options=sudo_options)
 
diff --git a/spython/utils/terminal.py b/spython/utils/terminal.py
index b844d9b7..1562925a 100644
--- a/spython/utils/terminal.py
+++ b/spython/utils/terminal.py
@@ -154,7 +154,7 @@ def run_command(
     no_newline_regexp="Progess",
     quiet=False,
     sudo_options=None,
-    env=None,
+    environ=None,
 ):
 
     """run_command uses subprocess to send a command to the terminal. If
@@ -181,7 +181,7 @@ def run_command(
 
     # Use the parent stdout and stderr
 
-    process = subprocess.Popen(cmd, stderr=subprocess.PIPE, stdout=stdout, env=env)
+    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
index 4d9d0dbb..7d716570 100644
--- 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"

From 75e6e672a51e91e558b1c3f5d33b74fb77cbb5ca Mon Sep 17 00:00:00 2001
From: Ceyda Cinarel <snu-ceyda@users.noreply.github.com>
Date: Tue, 15 Sep 2020 18:15:31 +0900
Subject: [PATCH 6/6] lint

---
 spython/instance/cmd/start.py | 7 ++++++-
 spython/main/base/command.py  | 7 ++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/spython/instance/cmd/start.py b/spython/instance/cmd/start.py
index e9ad9c69..ad6a5578 100644
--- a/spython/instance/cmd/start.py
+++ b/spython/instance/cmd/start.py
@@ -80,7 +80,12 @@ def start(
     self.cmd = cmd
 
     output = run_command(
-        cmd, sudo=sudo, sudo_options=sudo_options, quiet=True, capture=capture, environ=environ
+        cmd,
+        sudo=sudo,
+        sudo_options=sudo_options,
+        quiet=True,
+        capture=capture,
+        environ=environ,
     )
 
     if output["return_code"] == 0:
diff --git a/spython/main/base/command.py b/spython/main/base/command.py
index bc352021..53555782 100644
--- a/spython/main/base/command.py
+++ b/spython/main/base/command.py
@@ -131,7 +131,12 @@ def run_command(
         quiet = self.quiet
 
     result = run_cmd(
-        cmd, sudo=sudo, capture=capture, quiet=quiet, sudo_options=sudo_options, environ=environ
+        cmd,
+        sudo=sudo,
+        capture=capture,
+        quiet=quiet,
+        sudo_options=sudo_options,
+        environ=environ,
     )
 
     # If one line is returned, squash dimension