From 49da52286148dc834547fe2c138c215170841dd8 Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Thu, 27 Jul 2023 16:17:42 +1000
Subject: [PATCH] Add job script submission and generation step

This change adds a subcommand `fluxsite-submit-job` that writes the PBS
job to the file system and then submits the job to the queue. This
allows us to run the full fluxsite test by executing each step
separately, i.e. `benchcab checkout && benchcab build && benchcab
fluxsite-setup-work-dir && benchcab fluxsite-submit-job`.

Fixes #109
---
 benchcab/benchcab.py |  5 +++--
 benchcab/cli.py      | 30 ++++++++++++++++++++++++++----
 tests/test_cli.py    |  9 +++++++++
 3 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/benchcab/benchcab.py b/benchcab/benchcab.py
index 548ee031..6b04fc11 100644
--- a/benchcab/benchcab.py
+++ b/benchcab/benchcab.py
@@ -116,8 +116,6 @@ def _initialise_tasks(self) -> list[Task]:
         )
         return self.tasks
 
-    # TODO(Sean) this method should be the endpoint for the `fluxsite-submit-job`
-    # command line argument.
     def fluxsite_submit_job(self) -> None:
         """Submits the PBS job script step in the fluxsite test workflow."""
 
@@ -276,6 +274,9 @@ def main(self):
         if self.args.subcommand == "fluxsite-setup-work-dir":
             self.fluxsite_setup_work_directory()
 
+        if self.args.subcommand == "fluxsite-submit-job":
+            self.fluxsite_submit_job()
+
         if self.args.subcommand == "fluxsite-run-tasks":
             self.fluxsite_run_tasks()
 
diff --git a/benchcab/cli.py b/benchcab/cli.py
index 413946f9..2dc266d9 100644
--- a/benchcab/cli.py
+++ b/benchcab/cli.py
@@ -39,7 +39,10 @@ def generate_parser() -> argparse.ArgumentParser:
         action="store_true",
         help="Force benchcab to execute tasks on the current compute node.",
     )
-    args_run_subcommand.add_argument(
+
+    # parent parser that contains arguments common to all composite subcommands
+    args_composite_subcommand = argparse.ArgumentParser(add_help=False)
+    args_composite_subcommand.add_argument(
         "--skip",
         action="append",
         default=[],
@@ -68,7 +71,12 @@ def generate_parser() -> argparse.ArgumentParser:
     # subcommand: 'benchcab run'
     subparsers.add_parser(
         "run",
-        parents=[args_help, args_subcommand, args_run_subcommand],
+        parents=[
+            args_help,
+            args_subcommand,
+            args_run_subcommand,
+            args_composite_subcommand,
+        ],
         help="Run all test suites for CABLE.",
         description="""Runs all test suites for CABLE: fluxsite and spatial test suites. This
         command runs the full default set of tests for CABLE.""",
@@ -78,11 +86,16 @@ def generate_parser() -> argparse.ArgumentParser:
     # subcommand: 'benchcab fluxsite'
     subparsers.add_parser(
         "fluxsite",
-        parents=[args_help, args_subcommand, args_run_subcommand],
+        parents=[
+            args_help,
+            args_subcommand,
+            args_run_subcommand,
+            args_composite_subcommand,
+        ],
         help="Run the fluxsite test suite for CABLE.",
         description="""Runs the default fluxsite test suite for CABLE. This command is the
         equivalent of running 'benchcab checkout', 'benchcab build', 'benchcab
-        fluxsite-setup-work-dir', and 'benchcab fluxsite-run-tasks' sequentially.""",
+        fluxsite-setup-work-dir', and 'benchcab fluxsite-submit-job' sequentially.""",
         add_help=False,
     )
 
@@ -116,6 +129,15 @@ def generate_parser() -> argparse.ArgumentParser:
         add_help=False,
     )
 
+    # subcommand: 'benchcab fluxsite-submit-job'
+    subparsers.add_parser(
+        "fluxsite-submit-job",
+        parents=[args_help, args_subcommand, args_composite_subcommand],
+        help="Generate and submit the PBS job script for the fluxsite test suite.",
+        description="""Generates and submits the PBS job script for the fluxsite test suite.""",
+        add_help=False,
+    )
+
     # subcommand: 'benchcab fluxsite-run-tasks'
     subparsers.add_parser(
         "fluxsite-run-tasks",
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 96023bd8..df1d8ba9 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -45,6 +45,15 @@ def test_cli_parser():
         "verbose": False,
     }
 
+    # Success case: default fluxsite-submit-job command
+    res = vars(parser.parse_args(["fluxsite-submit-job"]))
+    assert res == {
+        "subcommand": "fluxsite-submit-job",
+        "config": "config.yaml",
+        "verbose": False,
+        "skip": [],
+    }
+
     # Success case: default fluxsite run-tasks command
     res = vars(parser.parse_args(["fluxsite-run-tasks"]))
     assert res == {