Rename flepimop batch to submit

Also corrected bugs in unit tests of `JobTimeLimit` with new
`BatchSystem` enum.

flepimop/gempyor_pkg/src/gempyor/batch.py

@@ -603,7 +603,7 @@ def _job_name(name: str | None, timestamp: datetime | None) -> str:
 
 
 @cli.command(
-    name="batch",
+    name="submit",
     params=[config_files_argument]
     + list(config_file_options.values())
     + [
@@ -739,7 +739,7 @@ def _job_name(name: str | None, timestamp: datetime | None) -> str:
     + list(verbosity_options.values()),
 )
 @click.pass_context
-def _click_batch(ctx: click.Context = mock_context, **kwargs) -> None:
+def _click_submit(ctx: click.Context = mock_context, **kwargs) -> None:
     """Submit batch jobs"""
     # Generic setup
     now = datetime.now(timezone.utc)
@@ -754,7 +754,7 @@ def _click_batch(ctx: click.Context = mock_context, **kwargs) -> None:
         or cfg["inference"]["method"].as_str() != "emcee"
     ):
         raise NotImplementedError(
-            "The `flepimop batch` CLI only supports EMCEE inference jobs."
+            "The `flepimop submit` CLI only supports EMCEE inference jobs."
         )
     inference_method = cfg["inference"]["method"].as_str()
     inference_method = (
@@ -776,7 +776,7 @@ def _click_batch(ctx: click.Context = mock_context, **kwargs) -> None:
     if batch_system != BatchSystem.SLURM:
         # Temporary limitation
         raise NotImplementedError(
-            "The `flepimop batch` CLI only supports batch submission to slurm."
+            "The `flepimop submit` CLI only supports batch submission to slurm."
         )
     logger.info("Constructing a job to submit to %s", batch_system)
     if batch_system != BatchSystem.SLURM and kwargs["email"] is not None:

flepimop/gempyor_pkg/tests/batch/test__click_batch.py → flepimop/gempyor_pkg/tests/batch/test__click_submit.py

@@ -6,7 +6,7 @@
 import pytest
 import yaml
 
-from gempyor.batch import _click_batch
+from gempyor.batch import _click_submit
 
 
 @pytest.fixture
@@ -34,13 +34,13 @@ def test_only_inference_emcee_supported_not_implemented_error(
         yaml.dump(config, f)
 
     runner = CliRunner()
-    result = runner.invoke(_click_batch, [str(config_file.absolute())])
+    result = runner.invoke(_click_submit, [str(config_file.absolute())])
 
     assert result.exit_code == 1
     assert isinstance(result.exception, NotImplementedError)
     assert (
         str(result.exception)
-        == "The `flepimop batch` CLI only supports EMCEE inference jobs."
+        == "The `flepimop submit` CLI only supports EMCEE inference jobs."
     )
 
 
@@ -55,13 +55,13 @@ def test_only_slurm_batch_system_supported_not_implemented_error(
         yaml.dump({"inference": {"method": "emcee"}}, f)
 
     runner = CliRunner()
-    result = runner.invoke(_click_batch, args + [str(config_file.absolute())])
+    result = runner.invoke(_click_submit, args + [str(config_file.absolute())])
 
     assert result.exit_code == 1
     assert isinstance(result.exception, NotImplementedError)
     assert (
         str(result.exception)
-        == "The `flepimop batch` CLI only supports batch submission to slurm."
+        == "The `flepimop submit` CLI only supports batch submission to slurm."
     )
 
 
@@ -72,7 +72,7 @@ def test_cluster_required_for_slurm_value_error(tmp_path: Path) -> None:
 
     runner = CliRunner()
     result = runner.invoke(
-        _click_batch,
+        _click_submit,
         [
             "--slurm",
             "--simulations",

flepimop/gempyor_pkg/tests/batch/test_job_time_limit_class.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from gempyor.batch import JobSize, JobTimeLimit
+from gempyor.batch import BatchSystem, JobSize, JobTimeLimit
 
 
 NONPOSITIVE_TIMEDELTAS = (timedelta(), timedelta(hours=-1.0), timedelta(days=-3.0))
@@ -31,14 +31,16 @@ def test_time_limit_non_positive_value_error(time_limit: timedelta) -> None:
         timedelta(minutes=12345),
     ),
 )
-@pytest.mark.parametrize("batch_system", (None, "aws", "local", "slurm"))
+@pytest.mark.parametrize(
+    "batch_system", (None, BatchSystem.AWS, BatchSystem.LOCAL, BatchSystem.SLURM)
+)
 def test_format_output_validation(
-    time_limit: timedelta, batch_system: Literal["aws", "local", "slurm"] | None
+    time_limit: timedelta, batch_system: BatchSystem | None
 ) -> None:
     job_time_limit = JobTimeLimit(time_limit=time_limit)
     formatted_time_limit = job_time_limit.format(batch_system=batch_system)
     assert isinstance(formatted_time_limit, str)
-    if batch_system == "slurm":
+    if batch_system == BatchSystem.SLURM:
         assert re.match(r"^[0-9]+\:[0-9]{2}\:[0-9]{2}$", formatted_time_limit)
     else:
         assert formatted_time_limit.isdigit()
@@ -50,15 +52,13 @@ def test_format_output_validation(
         (timedelta(hours=1), None, "60"),
         (timedelta(seconds=20), None, "1"),
         (timedelta(days=2, hours=3, minutes=45), None, "3105"),
-        (timedelta(hours=1), "slurm", "1:00:00"),
-        (timedelta(seconds=20), "slurm", "0:00:20"),
-        (timedelta(days=1, hours=2, minutes=34, seconds=5), "slurm", "26:34:05"),
+        (timedelta(hours=1), BatchSystem.SLURM, "1:00:00"),
+        (timedelta(seconds=20), BatchSystem.SLURM, "0:00:20"),
+        (timedelta(days=1, hours=2, minutes=34, seconds=5), BatchSystem.SLURM, "26:34:05"),
     ),
 )
 def test_format_exact_results(
-    time_limit: timedelta,
-    batch_system: Literal["aws", "local", "slurm"] | None,
-    expected: str,
+    time_limit: timedelta, batch_system: BatchSystem | None, expected: str
 ) -> None:
     job_time_limit = JobTimeLimit(time_limit=time_limit)
     assert job_time_limit.format(batch_system=batch_system) == expected