Expose the output_type option when streaming, and allow both stdout/s…

…tderr to be captured (#209)

* allow both output stdout stderr to be emitted. Expose option to allow capture
* updated changelog, version bump, error message
* added a basic stream test
* linting and pin black to 23.3.0

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: tgalvin <tim.galvin@csiro.au>
Co-authored-by: Tim Galvin <gal16b@petrichor-i1.cm.cluster>

.github/dev-requirements.txt

@@ -1,4 +1,4 @@
 pre-commit
-black
+black==23.3.0
 isort
 flake8

CHANGELOG.md

@@ -17,6 +17,7 @@ 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)
+ - exposed the stream type option, and ability to capture both stdout and stderr when stream=True (0.3.1)
  - dropping support for Singularity 2.x (0.3.0)
  - add comment out of STOPSIGNAL (0.2.14)
  - sudo `-E` flag should not be provided by default (0.2.13)

setup.py

@@ -75,7 +75,6 @@ def get_requirements(lookup=None):
 
 
 if __name__ == "__main__":
-
     INSTALL_REQUIRES = get_requirements(lookup)
     TESTS_REQUIRES = get_requirements(lookup)
 

spython/client/__init__.py

@@ -13,7 +13,6 @@
 
 
 def get_parser():
-
     parser = argparse.ArgumentParser(
         description="Singularity Client",
         formatter_class=argparse.RawTextHelpFormatter,
@@ -147,7 +146,6 @@ def version():
 
 
 def main():
-
     parser = get_parser()
 
     def print_help(return_code=0):

spython/client/recipe.py

@@ -74,7 +74,6 @@ def main(args, options, parser):
         force = True
 
     if args.json:
-
         if outfile is not None:
             if not os.path.exists(outfile):
                 if force:
@@ -85,7 +84,6 @@ def main(args, options, parser):
             print(json.dumps(recipeParser.recipe.json(), indent=4))
 
     else:
-
         # Do the conversion
         recipeWriter = writer(recipeParser.recipe)
         result = recipeWriter.convert(runscript=entrypoint, force=force)

spython/instance/__init__.py

@@ -93,7 +93,6 @@ def _update_metadata(self, kwargs=None):
 
         # Add acceptable arguments
         for arg in ["pid", "name", "ip_address", "log_err_path", "log_out_path", "img"]:
-
             # Skip over non-iterables:
             if arg in kwargs:
                 setattr(self, arg, kwargs[arg])

spython/instance/cmd/start.py

@@ -49,7 +49,6 @@ def start(
 
     # If an image isn't provided, we have an initialized instance
     if image is None:
-
         # Not having this means it was called as a command, without an image
         if not hasattr(self, "_image"):
             bot.exit("Please provide an image, or create an Instance first.")

spython/main/base/command.py

@@ -66,7 +66,6 @@ def generate_bind_list(self, bindlist=None):
         bindlist = bindlist.split(" ")
 
     for bind in bindlist:
-
         # Still cannot be None
         if bind:
             bot.debug("Adding bind %s" % bind)
@@ -113,7 +112,6 @@ def run_command(
     environ=None,
     background=False,
 ):
-
     """
     Run_command is a wrapper for the global run_command, checking first
     for sudo and exiting on error if needed. The message is returned as

spython/main/base/generate.py

@@ -11,7 +11,6 @@
 
 
 class RobotNamer:
-
     _descriptors = [
         "chunky",
         "buttery",

spython/main/build.py

@@ -31,7 +31,6 @@ def build(
     sudo_options=None,
     singularity_options=None,
 ):
-
     """build a singularity image, optionally for an isolated build
     (requires sudo). If you specify to stream, expect the image name
     and an iterator to be returned.

spython/main/execute.py

@@ -29,6 +29,7 @@ def execute(
     sudo_options=None,
     quiet=True,
     environ=None,
+    stream_type="stdout",
 ):
     """execute: send a command to a container
 
@@ -51,6 +52,7 @@ def execute(
                    and message result not (default)
     quiet: Do not print verbose output.
     environ: extra environment to add.
+    stream_type: Sets which output stream from the singularity command should be return. Values are 'stdout', 'stderr', 'both'.
     """
     from spython.utils import check_install
 
@@ -68,7 +70,6 @@ def execute(
         image = None
 
     if command is not None:
-
         # No image provided, default to use the client's loaded image
         if image is None:
             image = self._get_uri()
@@ -115,7 +116,9 @@ def execute(
                 quiet=quiet,
                 environ=environ,
             )
-        return stream_command(cmd, sudo=sudo, sudo_options=sudo_options)
+        return stream_command(
+            cmd, sudo=sudo, sudo_options=sudo_options, output_type=stream_type
+        )
 
     bot.exit("Please include a command (list) to execute.")
 

spython/main/export.py

@@ -19,7 +19,6 @@ def export(
     sudo=False,
     singularity_options=None,
 ):
-
     """export will export an image, sudo must be used. Since we have Singularity
     versions after 3, export is replaced with building into a sandbox.
 

spython/main/instances.py

@@ -63,15 +63,13 @@ def list_instances(
     # Success, we have instances
 
     if output["return_code"] == 0:
-
         instances = json.loads(output["message"][0]).get("instances", {})
 
         # Does the user want instance objects instead?
         listing = []
 
         if not return_json:
             for i in instances:
-
                 # If the user has provided a name, only add instance matches
                 if name is not None:
                     if name != i["instance"]:

spython/main/parse/parsers/base.py

@@ -48,7 +48,6 @@ def __init__(self, filename, load=True):
         self.recipe = {"spython-base": Recipe(self.filename)}
 
         if self.filename:
-
             # Read in the raw lines of the file
             self.lines = read_file(self.filename)
 
@@ -69,7 +68,6 @@ def _run_checks(self):
         attempting parsing.
         """
         if self.filename is not None:
-
             # Does the recipe provided exist?
             if not os.path.exists(self.filename):
                 bot.exit("Cannot find %s, is the path correct?" % self.filename)

spython/main/parse/parsers/docker.py

@@ -14,7 +14,6 @@
 
 
 class DockerParser(ParserBase):
-
     name = "docker"
 
     def __init__(self, filename="Dockerfile", load=True):
@@ -49,7 +48,6 @@ def parse(self):
         previous = None
 
         for line in self.lines:
-
             parser = self._get_mapping(line, parser, previous)
 
             # Parse it, if appropriate
@@ -147,7 +145,6 @@ def _arg(self, line):
 
         # Try to extract arguments from the line
         for arg in line:
-
             # An undefined arg cannot be used
             if "=" not in arg:
                 bot.warning(
@@ -197,15 +194,13 @@ def parse_env(self, envlist):
         exports = []
 
         for env in envlist:
-
             pieces = re.split("( |\\\".*?\\\"|'.*?')", env)
             pieces = [p for p in pieces if p.strip()]
 
             while pieces:
                 current = pieces.pop(0)
 
                 if current.endswith("="):
-
                     # Case 1: ['A='] --> A=
                     nextone = ""
 
@@ -243,7 +238,6 @@ def _copy(self, lines):
         lines = self._setup("COPY", lines)
 
         for line in lines:
-
             # Take into account multistage builds
             layer = None
             if line.startswith("--from"):

spython/main/parse/parsers/singularity.py

@@ -13,7 +13,6 @@
 
 
 class SingularityParser(ParserBase):
-
     name = "singularity"
 
     def __init__(self, filename="Singularity", load=True):
@@ -51,7 +50,6 @@ def _setup(self, lines):
         bot.warning("SETUP is error prone, please check output.")
 
         for line in lines:
-
             # For all lines, replace rootfs with actual root /
             line = re.sub("[$]{?SINGULARITY_ROOTFS}?", "", "$SINGULARITY_ROOTFS")
 
@@ -171,7 +169,6 @@ def _run(self, lines):
 
         # Multiple line runscript needs multiple lines written to script
         if len(lines) > 1:
-
             bot.warning("More than one line detected for runscript!")
             bot.warning("These will be echoed into a single script to call.")
             self._write_script("/entrypoint.sh", lines)
@@ -257,7 +254,6 @@ def _load_section(self, lines, section, layer=None):
         members = []
 
         while True:
-
             if not lines:
                 break
             next_line = lines[0]
@@ -278,7 +274,6 @@ def _load_section(self, lines, section, layer=None):
 
         # Add the list to the config
         if members and section is not None:
-
             # Get the correct parsing function
             parser = self._get_mapping(section)
 
@@ -309,7 +304,6 @@ def load_recipe(self):
         comments = []
 
         while lines:
-
             # Clean up white trailing/leading space
             line = lines.pop(0)
             stripped = line.strip()

spython/main/parse/recipe.py

@@ -23,7 +23,6 @@ class Recipe:
     """
 
     def __init__(self, recipe=None, layer=1):
-
         self.cmd = None
         self.comments = []
         self.entrypoint = None

spython/main/parse/writers/docker.py

@@ -45,7 +45,6 @@
 
 
 class DockerWriter(WriterBase):
-
     name = "docker"
 
     def __init__(self, recipe=None):  # pylint: disable=useless-super-delegation
@@ -161,7 +160,6 @@ def write_lines(label, lines):
     result = []
     continued = False
     for line in lines:
-
         # Skip comments and empty lines
         if line.strip() == "" or line.strip().startswith("#"):
             continue

spython/main/parse/writers/singularity.py

@@ -13,7 +13,6 @@
 
 
 class SingularityWriter(WriterBase):
-
     name = "singularity"
 
     def __init__(self, recipe=None):  # pylint: disable=useless-super-delegation
@@ -52,7 +51,6 @@ def convert(self, runscript="/bin/bash", force=False):
 
         # Write each layer to new file
         for stage, parser in self.recipe.items():
-
             # Set the first and active stage
             self.stage = stage
 
@@ -111,9 +109,7 @@ def _create_runscript(self, default="/bin/bash", force=False):
 
         # Only look at Docker if not enforcing default
         if not force:
-
             if self.recipe[self.stage].entrypoint is not None:
-
                 # The provided entrypoint can be a string or a list
                 if isinstance(self.recipe[self.stage].entrypoint, list):
                     entrypoint = " ".join(self.recipe[self.stage].entrypoint)

spython/main/pull.py

@@ -24,7 +24,6 @@ def pull(
     quiet=False,
     singularity_options=None,
 ):
-
     """pull will pull a singularity hub or Docker image
 
     Parameters
@@ -92,7 +91,6 @@ def pull(
 
         # Option 3: A custom name we can predict (not commit/hash) and can also show
         else:
-
             # As of Singularity 3.x (at least 3.8) output goes to stderr
             return final_image, stream_command(cmd, sudo=False, output_type="stderr")
 

spython/oci/__init__.py

@@ -9,7 +9,6 @@
 
 
 class OciImage(ImageBase):
-
     # Default functions of client don't use sudo
     sudo = False
 

spython/oci/cmd/actions.py

@@ -19,7 +19,6 @@ def run(
     singularity_options=None,
     log_format="kubernetes",
 ):
-
     """run is a wrapper to create, start, attach, and delete a container.
 
     Equivalent command line example:
@@ -57,7 +56,6 @@ def create(
     log_format="kubernetes",
     singularity_options=None,
 ):
-
     """use the client to create a container from a bundle directory. The bundle
     directory should have a config.json. You must be the root user to
     create a runtime.
@@ -104,7 +102,6 @@ def _run(
     log_format="kubernetes",
     singularity_options=None,
 ):
-
     """_run is the base function for run and create, the only difference
     between the two being that run does not have an option for sync_socket.