junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -5,49 +5,12 @@
 
 import logging
 from pathlib import Path
-from typing import Optional, Union
 
 import pytest
 
 from junifer.api.queue_context import HTCondorAdapter
 
 
-def test_HTCondorAdapter_env_kind_error() -> None:
-    """Test error for invalid env kind."""
-    with pytest.raises(ValueError, match=r"Invalid value for `env.kind`"):
-        HTCondorAdapter(
-            job_name="check_env_kind",
-            job_dir=Path("."),
-            yaml_config_path=Path("."),
-            elements=["sub01"],
-            env={"kind": "jambalaya"},
-        )
-
-
-def test_HTCondorAdapter_env_shell_error() -> None:
-    """Test error for invalid env shell."""
-    with pytest.raises(ValueError, match=r"Invalid value for `env.shell`"):
-        HTCondorAdapter(
-            job_name="check_env_shell",
-            job_dir=Path("."),
-            yaml_config_path=Path("."),
-            elements=["sub01"],
-            env={"kind": "conda", "shell": "fish"},
-        )
-
-
-def test_HTCondorAdapter_collect_error() -> None:
-    """Test error for invalid collect option."""
-    with pytest.raises(ValueError, match=r"Invalid value for `collect`"):
-        HTCondorAdapter(
-            job_name="check_collect",
-            job_dir=Path("."),
-            yaml_config_path=Path("."),
-            elements=["sub01"],
-            collect="off",
-        )
-
-
 @pytest.mark.parametrize(
     "pre_run, expected_text, shell",
     [
@@ -58,7 +21,7 @@ def test_HTCondorAdapter_collect_error() -> None:
     ],
 )
 def test_HTCondorAdapter_pre_run(
-    pre_run: Optional[str],
+    pre_run: str | None,
     expected_text: str,
     shell: str,
 ) -> None:
@@ -82,8 +45,8 @@ def test_HTCondorAdapter_pre_run(
         env={"kind": "conda", "name": "junifer", "shell": shell},
         pre_run=pre_run,
     )
-    assert shell in adapter.pre_run()
-    assert expected_text in adapter.pre_run()
+    assert shell in adapter.pre_run_cmds()
+    assert expected_text in adapter.pre_run_cmds()
 
 
 @pytest.mark.parametrize(
@@ -100,7 +63,7 @@ def test_HTCondorAdapter_pre_run(
     ],
 )
 def test_HTCondorAdapter_pre_collect(
-    pre_collect: Optional[str],
+    pre_collect: str | None,
     expected_text: str,
     collect: str,
     shell: str,
@@ -126,10 +89,10 @@ def test_HTCondorAdapter_pre_collect(
         elements=["sub01"],
         env={"kind": "venv", "name": "junifer", "shell": shell},
         pre_collect=pre_collect,
-        collect=collect,
+        collect_task=collect,
     )
-    assert shell in adapter.pre_collect()
-    assert expected_text in adapter.pre_collect()
+    assert shell in adapter.pre_collect_cmds()
+    assert expected_text in adapter.pre_collect_cmds()
 
 
 @pytest.mark.parametrize(
@@ -140,7 +103,7 @@ def test_HTCondorAdapter_pre_collect(
     ],
 )
 def test_HTCondorAdapter_run_collect(
-    extra_preamble: Optional[str], expected_text: str
+    extra_preamble: str | None, expected_text: str
 ) -> None:
     """Test HTCondorAdapter run() and collect().
 
@@ -159,8 +122,8 @@ def test_HTCondorAdapter_run_collect(
         elements=["sub01"],
         extra_preamble=extra_preamble,
     )
-    assert expected_text in adapter.run()
-    assert expected_text in adapter.collect()
+    assert expected_text in adapter.run_cmds()
+    assert expected_text in adapter.collect_cmds()
 
 
 @pytest.mark.parametrize(
@@ -181,7 +144,7 @@ def test_HTCondorAdapter_run_collect(
     ],
 )
 def test_HTCondor_dag(
-    elements: list[Union[str, tuple]], collect: str, expected_text: str
+    elements: list[str | tuple], collect: str, expected_text: str
 ) -> None:
     """Test HTCondorAdapter dag().
 
@@ -200,9 +163,9 @@ def test_HTCondor_dag(
         job_dir=Path("."),
         yaml_config_path=Path("."),
         elements=elements,
-        collect=collect,
+        collect_task=collect,
     )
-    assert expected_text in adapter.dag()
+    assert expected_text in adapter.dag_cmds()
 
 
 @pytest.mark.parametrize(

junifer/api/res/fsl/run_fsl_docker.sh

@@ -34,6 +34,10 @@ echo "Docker args: ${docker_args[*]}" >&2
 echo "Corrected args for FSL: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
+# Pass the output type, as FSL writes it instead of the type of the extension
+if [ -n "${FSLOUTPUTTYPE}" ]; then
+    docker_args+=("-e FSLOUTPUTTYPE=${FSLOUTPUTTYPE}")
+fi
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"
 echo "Running command: ${cmd}" >&2
 ${cmd}