feat: CLI options can be supplied using env vars

Although sbatch already allows providing values for options through SBATCH_ prefixed env vars, not all options are supported. This change adds support for all options of sbatch through a GRIDTK_SUBMIT_ prefix. For example, to always get emails when a job finishes, you can set GRIDTK_SUBMIT_MAIL_USER to your email address and GRIDTK_SUBMIT_MAIL_TYPE to END. This is useful when you have a set of options that you always want to use, but don't want to specify them every time you submit a job.

Author: 183amir

README.md

@@ -198,6 +198,26 @@ This is a fast, convenient, and **recommended** way to submit a job without havi
 script and since everything is tracked by GridTK, you still benefit from the same
 reproducibility guarantees.
 
+### Environment Variables for CLI Options
+
+While sbatch already allows providing values for some options through `SBATCH_` prefixed environment variables, not all options are supported. GridTK adds support for all CLI options through the `GRIDTK_SUBMIT_` prefix. For example:
+
+```bash
+# Set default email notification settings
+export GRIDTK_SUBMIT_MAIL_USER=your.email@example.com
+export GRIDTK_SUBMIT_MAIL_TYPE=END
+
+# Use debug partition by default
+export GRIDTK_SUBMIT_PARTITION=debug
+
+# Now submit a job - it will use these settings automatically
+gridtk submit job.sh
+```
+
+This is useful when you have a set of options that you always want to use, but don't want to specify them every time you submit a job.
+
+Of course, other gridtk commands such as `gridtk resubmit` options can also be set using environment variables like: `export GRIDTK_RESUBMIT_STATE=ALL`.
+
 ### Job Dependencies
 
 To submit a job that depends on another job, use the `--dependency` flag:

src/gridtk/cli.py

@@ -142,6 +142,7 @@ def _job_filters_decorator(function):
     context_settings={
         "show_default": True,
         "help_option_names": ["--help", "-h"],
+        "auto_envvar_prefix": "GRIDTK",
     },
 )
 @click.option(

tests/test_gridtk.py

@@ -202,6 +202,45 @@ def test_submit_wrap(mock_check_output, runner):
     )
 
 
+@patch("subprocess.check_output")
+def test_submit_with_env_vars(mock_check_output: Mock, runner):
+    """Test that environment variables with GRIDTK_SUBMIT_ prefix are properly converted to CLI options."""
+    mock_check_output.return_value = _sbatch_output(123456789)
+    with runner.isolated_filesystem():
+        result = runner.invoke(
+            cli,
+            ["submit", "job.sh"],
+            env={
+                "GRIDTK_SUBMIT_MAIL_USER": "test@example.com",
+                "GRIDTK_SUBMIT_MAIL_TYPE": "END",
+                "GRIDTK_SUBMIT_PARTITION": "debug",
+            },
+        )
+
+        assert_click_runner_result(result)
+        assert "1" in result.output
+
+    mock_check_output.assert_called_with(
+        [
+            "sbatch",
+            "--job-name",
+            "gridtk",
+            "--output",
+            "logs/gridtk.%j.out",
+            "--error",
+            "logs/gridtk.%j.out",
+            "--mail-type",
+            "END",
+            "--mail-user",
+            "test@example.com",
+            "--partition",
+            "debug",
+            "job.sh",
+        ],
+        text=True,
+    )
+
+
 @patch("subprocess.check_output")
 def test_submit_triple_dash(mock_check_output: Mock, runner):
     mock_check_output.return_value = _sbatch_output(123456789)