docs/changes/newsfragments/503.enh

@@ -0,0 +1 @@
+Revert ``pre_run`` and ``pre_collect`` parameters for queue context adapters by `Synchon Mandal`_

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -35,9 +35,9 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         The path to the YAML config file.
     elements : ``Elements``
         Element(s) to process. Will be used to index the DataGrabber.
-    pre_run_cmds : str or None, optional
+    pre_run : str or None, optional
         Extra shell commands to source before the run (default None).
-    pre_collect_cmds : str or None, optional
+    pre_collect : str or None, optional
         Extra shell commands to source before the collect (default None).
     env : :class:`.QueueContextEnv` or None, optional
         The environment configuration. If None, will run without a
@@ -63,8 +63,8 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     job_dir: Path
     yaml_config_path: Path
     elements: Elements
-    pre_run_cmds: str | None = None
-    pre_collect_cmds: str | None = None
+    pre_run: str | None = None
+    pre_collect: str | None = None
     env: QueueContextEnv | None = None
     verbose: str = "info"
     verbose_datalad: str | None = None
@@ -105,7 +105,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
 
         return "\n".join(elements_to_run)
 
-    def pre_run(self) -> str:
+    def pre_run_cmds(self) -> str:
         """Return pre-run commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
@@ -113,10 +113,10 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             "# Force datalad to run in non-interactive mode\n"
             "DATALAD_UI_INTERACTIVE=false\n"
         )
-        var = self.pre_run_cmds or ""
+        var = self.pre_run or ""
         return fixed + "\n" + var
 
-    def run(self) -> str:
+    def run_cmds(self) -> str:
         """Return run commands."""
         verbose_args = f"--verbose {self.verbose}"
         if self.verbose_datalad:
@@ -141,16 +141,16 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"--element"
         )
 
-    def pre_collect(self) -> str:
+    def pre_collect_cmds(self) -> str:
         """Return pre-collect commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
             "# This script is auto-generated by junifer.\n"
         )
-        var = self.pre_collect_cmds or ""
+        var = self.pre_collect or ""
         return fixed + "\n" + var
 
-    def collect(self) -> str:
+    def collect_cmds(self) -> str:
         """Return collect commands."""
         verbose_args = f"--verbose {self.verbose}"
         if self.verbose_datalad:
@@ -196,14 +196,14 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"Writing {self._pre_run_path.name} to {self.job_dir.resolve()!s}"
         )
         self._pre_run_path.touch()
-        self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
+        self._pre_run_path.write_text(textwrap.dedent(self.pre_run_cmds()))
         make_executable(self._pre_run_path)
         # Create run
         logger.info(
             f"Writing {self._run_path.name} to {self.job_dir.resolve()!s}"
         )
         self._run_path.touch()
-        self._run_path.write_text(textwrap.dedent(self.run()))
+        self._run_path.write_text(textwrap.dedent(self.run_cmds()))
         make_executable(self._run_path)
         # Create pre collect
         logger.info(
@@ -211,14 +211,16 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"{self.job_dir.resolve()!s}"
         )
         self._pre_collect_path.touch()
-        self._pre_collect_path.write_text(textwrap.dedent(self.pre_collect()))
+        self._pre_collect_path.write_text(
+            textwrap.dedent(self.pre_collect_cmds())
+        )
         make_executable(self._pre_collect_path)
         # Create collect
         logger.info(
             f"Writing {self._collect_path.name} to {self.job_dir.resolve()!s}"
         )
         self._collect_path.touch()
-        self._collect_path.write_text(textwrap.dedent(self.collect()))
+        self._collect_path.write_text(textwrap.dedent(self.collect_cmds()))
         make_executable(self._collect_path)
         # Submit if required
         run_cmd = f"sh {self._run_path.resolve()!s}"

junifer/api/queue_context/htcondor_adapter.py

@@ -52,9 +52,9 @@ class HTCondorAdapter(QueueContextAdapter):
         The path to the YAML config file.
     elements : ``Elements``
         Element(s) to process. Will be used to index the DataGrabber.
-    pre_run_cmds : str or None, optional
+    pre_run : str or None, optional
         Extra shell commands to source before the run (default None).
-    pre_collect_cmds : str or None, optional
+    pre_collect : str or None, optional
         Extra shell commands to source before the collect (default None).
     env : :class:`.QueueContextEnv` or None, optional
         The environment configuration. If None, will run without a
@@ -91,8 +91,8 @@ class HTCondorAdapter(QueueContextAdapter):
     job_dir: Path
     yaml_config_path: Path
     elements: Elements
-    pre_run_cmds: str | None = None
-    pre_collect_cmds: str | None = None
+    pre_run: str | None = None
+    pre_collect: str | None = None
     env: QueueContextEnv | None = None
     verbose: str = "info"
     verbose_datalad: str | None = None
@@ -127,7 +127,7 @@ class HTCondorAdapter(QueueContextAdapter):
         )
         self._dag_path = self.job_dir / f"{self.job_name}.dag"
 
-    def pre_run(self) -> str:
+    def pre_run_cmds(self) -> str:
         """Return pre-run commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
@@ -135,10 +135,10 @@ class HTCondorAdapter(QueueContextAdapter):
             "# Force datalad to run in non-interactive mode\n"
             "DATALAD_UI_INTERACTIVE=false\n"
         )
-        var = self.pre_run_cmds or ""
+        var = self.pre_run or ""
         return fixed + "\n" + var
 
-    def run(self) -> str:
+    def run_cmds(self) -> str:
         """Return run commands."""
         verbose_args = f"--verbose {self.verbose} "
         if self.verbose_datalad is not None:
@@ -176,19 +176,19 @@ class HTCondorAdapter(QueueContextAdapter):
         var = self.extra_preamble or ""
         return fixed + "\n" + var + "\n" + "queue"
 
-    def pre_collect(self) -> str:
+    def pre_collect_cmds(self) -> str:
         """Return pre-collect commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
             "# This script is auto-generated by junifer.\n"
         )
-        var = self.pre_collect_cmds or ""
+        var = self.pre_collect or ""
         # Add commands if collect="yes"
         if self.collect_task == "yes":
             var += 'if [ "${1}" == "4" ]; then\n    exit 1\nfi\n'
         return fixed + "\n" + var
 
-    def collect(self) -> str:
+    def collect_cmds(self) -> str:
         """Return collect commands."""
         verbose_args = f"--verbose {self.verbose} "
         if self.verbose_datalad is not None:
@@ -222,7 +222,7 @@ class HTCondorAdapter(QueueContextAdapter):
         var = self.extra_preamble or ""
         return fixed + "\n" + var + "\n" + "queue"
 
-    def dag(self) -> str:
+    def dag_cmds(self) -> str:
         """Return HTCondor DAG commands."""
         fixed = ""
         for idx, element in enumerate(self.elements):
@@ -277,7 +277,7 @@ class HTCondorAdapter(QueueContextAdapter):
             f"Writing {self._pre_run_path.name} to {self.job_dir.resolve()!s}"
         )
         self._pre_run_path.touch()
-        self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
+        self._pre_run_path.write_text(textwrap.dedent(self.pre_run_cmds()))
         make_executable(self._pre_run_path)
         # Create run
         logger.debug(
@@ -285,14 +285,16 @@ class HTCondorAdapter(QueueContextAdapter):
             f"{self.job_dir.resolve()!s}"
         )
         self._submit_run_path.touch()
-        self._submit_run_path.write_text(textwrap.dedent(self.run()))
+        self._submit_run_path.write_text(textwrap.dedent(self.run_cmds()))
         # Create pre collect
         logger.info(
             f"Writing {self._pre_collect_path.name} to "
             f"{self.job_dir.resolve()!s}"
         )
         self._pre_collect_path.touch()
-        self._pre_collect_path.write_text(textwrap.dedent(self.pre_collect()))
+        self._pre_collect_path.write_text(
+            textwrap.dedent(self.pre_collect_cmds())
+        )
         make_executable(self._pre_collect_path)
         # Create collect
         logger.debug(
@@ -300,13 +302,15 @@ class HTCondorAdapter(QueueContextAdapter):
             f"{self.job_dir.resolve()!s}"
         )
         self._submit_collect_path.touch()
-        self._submit_collect_path.write_text(textwrap.dedent(self.collect()))
+        self._submit_collect_path.write_text(
+            textwrap.dedent(self.collect_cmds())
+        )
         # Create DAG
         logger.debug(
             f"Writing {self._dag_path.name} to {self.job_dir.resolve()!s}"
         )
         self._dag_path.touch()
-        self._dag_path.write_text(textwrap.dedent(self.dag()))
+        self._dag_path.write_text(textwrap.dedent(self.dag_cmds()))
         # Submit if required
         condor_submit_dag_cmd = [
             "condor_submit_dag",

junifer/api/queue_context/queue_context_adapter.py

@@ -64,11 +64,11 @@ class QueueContextAdapter(BaseModel, ABC):
 
     model_config = ConfigDict(
         use_enum_values=True,
-        extra="allow",
+        extra="forbid",
     )
 
     @abstractmethod
-    def pre_run(self) -> str:
+    def pre_run_cmds(self) -> str:
         """Return pre-run commands."""
         raise_error(
             msg="Concrete classes need to implement pre_run()",
@@ -76,7 +76,7 @@ class QueueContextAdapter(BaseModel, ABC):
         )
 
     @abstractmethod
-    def run(self) -> str:
+    def run_cmds(self) -> str:
         """Return run commands."""
         raise_error(
             msg="Concrete classes need to implement run()",
@@ -84,7 +84,7 @@ class QueueContextAdapter(BaseModel, ABC):
         )
 
     @abstractmethod
-    def pre_collect(self) -> str:
+    def pre_collect_cmds(self) -> str:
         """Return pre-collect commands."""
         raise_error(
             msg="Concrete classes need to implement pre_collect()",
@@ -92,7 +92,7 @@ class QueueContextAdapter(BaseModel, ABC):
         )
 
     @abstractmethod
-    def collect(self) -> str:
+    def collect_cmds(self) -> str:
         """Return collect commands."""
         raise_error(
             msg="Concrete classes need to implement collect()",

junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py

@@ -73,10 +73,10 @@ def test_GnuParallelLocalAdapter_pre_run(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "conda", "name": "junifer", "shell": shell},
-        pre_run_cmds=pre_run,
+        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(
@@ -111,10 +111,10 @@ def test_GnuParallelLocalAdapter_pre_collect(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "venv", "name": "junifer", "shell": shell},
-        pre_collect_cmds=pre_collect,
+        pre_collect=pre_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()
 
 
 def test_GnuParallelLocalAdapter_run() -> None:
@@ -125,7 +125,7 @@ def test_GnuParallelLocalAdapter_run() -> None:
         yaml_config_path=Path("."),
         elements=["sub01"],
     )
-    assert "run" in adapter.run()
+    assert "run" in adapter.run_cmds()
 
 
 def test_GnuParallelLocalAdapter_collect() -> None:
@@ -136,7 +136,7 @@ def test_GnuParallelLocalAdapter_collect() -> None:
         yaml_config_path=Path("."),
         elements=["sub01"],
     )
-    assert "collect" in adapter.collect()
+    assert "collect" in adapter.collect_cmds()
 
 
 @pytest.mark.parametrize(

junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -43,10 +43,10 @@ def test_HTCondorAdapter_pre_run(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "conda", "name": "junifer", "shell": shell},
-        pre_run_cmds=pre_run,
+        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(
@@ -88,11 +88,11 @@ def test_HTCondorAdapter_pre_collect(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "venv", "name": "junifer", "shell": shell},
-        pre_collect_cmds=pre_collect,
+        pre_collect=pre_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(
@@ -122,8 +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(
@@ -165,7 +165,7 @@ def test_HTCondor_dag(
         elements=elements,
         collect_task=collect,
     )
-    assert expected_text in adapter.dag()
+    assert expected_text in adapter.dag_cmds()
 
 
 @pytest.mark.parametrize(