docs/changes/newsfragments/273.feature

@@ -0,0 +1 @@
+Add support for choosing between ``bash`` and ``zsh`` shells when queueing by `Synchon Mandal`_

docs/changes/newsfragments/320.fix

@@ -1 +0,0 @@
-Add a validation step on the :func:`.run` function to validate the marker collection by `Fede Raimondo`_

docs/changes/newsfragments/321.fix

@@ -1 +0,0 @@
-Add the executable flag to the ants docker scripts, fsl docker scripts and other running scripts by `Fede Raimondo_`

docs/whats_new.rst

@@ -46,6 +46,10 @@ Bugfixes
   (:gh:`312`)
 - Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon
   Mandal`_ (:gh:`314`)
+- Add a validation step on the :func:`.run` function to validate the marker
+  collection by `Fede Raimondo`_ (:gh:`320`)
+- Add the executable flag to the ants docker scripts, fsl docker scripts and
+  other running scripts by `Fede Raimondo`_ (:gh:`321`)
 - Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_
   (:gh:`322`)
 

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -43,7 +43,8 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     Raises
     ------
     ValueError
-        If``env`` is invalid.
+        If ``env.kind`` is invalid or
+        if ``env.shell`` is invalid.
 
     See Also
     --------
@@ -110,13 +111,22 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
                 f"must be one of {valid_env_kinds}"
             )
         else:
+            # Check shell
+            shell = env.get("shell", "bash")
+            valid_shells = ["bash", "zsh"]
+            if shell not in valid_shells:
+                raise_error(
+                    f"Invalid value for `env.shell`: {shell}, "
+                    f"must be one of {valid_shells}"
+                )
+            self._shell = shell
             # Set variables
             if env["kind"] == "local":
                 # No virtual environment
                 self._executable = "junifer"
                 self._arguments = ""
             else:
-                self._executable = f"run_{env['kind']}.sh"
+                self._executable = f"run_{env['kind']}.{self._shell}"
                 self._arguments = f"{env['name']} junifer"
                 self._exec_path = self._job_dir / self._executable
 
@@ -135,7 +145,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     def pre_run(self) -> str:
         """Return pre-run commands."""
         fixed = (
-            "#!/usr/bin/env bash\n\n"
+            f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n\n"
             "# Force datalad to run in non-interactive mode\n"
             "DATALAD_UI_INTERACTIVE=false\n"
@@ -146,7 +156,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     def run(self) -> str:
         """Return run commands."""
         return (
-            "#!/usr/bin/env bash\n\n"
+            f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n\n"
             "# Run pre_run.sh\n"
             f"sh {self._pre_run_path.resolve()!s}\n\n"
@@ -166,7 +176,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     def pre_collect(self) -> str:
         """Return pre-collect commands."""
         fixed = (
-            "#!/usr/bin/env bash\n\n"
+            f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n"
         )
         var = self._pre_collect or ""
@@ -175,7 +185,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     def collect(self) -> str:
         """Return collect commands."""
         return (
-            "#!/usr/bin/env bash\n\n"
+            f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n\n"
             "# Run pre_collect.sh\n"
             f"sh {self._pre_collect_path.resolve()!s}\n\n"

junifer/api/queue_context/htcondor_adapter.py

@@ -126,7 +126,8 @@ class HTCondorAdapter(QueueContextAdapter):
         Raises
         ------
         ValueError
-            If ``env.kind`` is invalid.
+            If ``env.kind`` is invalid or
+            if ``env.shell`` is invalid.
 
         """
         # Set env related variables
@@ -140,13 +141,22 @@ class HTCondorAdapter(QueueContextAdapter):
                 f"must be one of {valid_env_kinds}"
             )
         else:
+            # Check shell
+            shell = env.get("shell", "bash")
+            valid_shells = ["bash", "zsh"]
+            if shell not in valid_shells:
+                raise_error(
+                    f"Invalid value for `env.shell`: {shell}, "
+                    f"must be one of {valid_shells}"
+                )
+            self._shell = shell
             # Set variables
             if env["kind"] == "local":
                 # No virtual environment
                 self._executable = "junifer"
                 self._arguments = ""
             else:
-                self._executable = f"run_{env['kind']}.sh"
+                self._executable = f"run_{env['kind']}.{self._shell}"
                 self._arguments = f"{env['name']} junifer"
                 self._exec_path = self._job_dir / self._executable
 
@@ -181,7 +191,7 @@ class HTCondorAdapter(QueueContextAdapter):
     def pre_run(self) -> str:
         """Return pre-run commands."""
         fixed = (
-            "#!/bin/bash\n\n"
+            f"#!/usr/bin/env {self._shell}\n\n"
             "# This script is auto-generated by junifer.\n\n"
             "# Force datalad to run in non-interactive mode\n"
             "DATALAD_UI_INTERACTIVE=false\n"
@@ -225,12 +235,13 @@ class HTCondorAdapter(QueueContextAdapter):
     def pre_collect(self) -> str:
         """Return pre-collect commands."""
         fixed = (
-            "#!/bin/bash\n\n" "# This script is auto-generated by junifer.\n"
+            f"#!/usr/bin/env {self._shell}\n\n"
+            "# This script is auto-generated by junifer.\n"
         )
         var = self._pre_collect or ""
         # Add commands if collect="yes"
         if self._collect == "yes":
-            var += 'if [ "${1}" == "4" ]; then\n' "    exit 1\n" "fi\n"
+            var += 'if [ "${1}" == "4" ]; then\n    exit 1\nfi\n'
         return fixed + "\n" + var
 
     def collect(self) -> str:

junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py

@@ -12,11 +12,11 @@ import pytest
 from junifer.api.queue_context import GnuParallelLocalAdapter
 
 
-def test_GnuParallelLocalAdapter_env_error() -> None:
+def test_GnuParallelLocalAdapter_env_kind_error() -> None:
     """Test error for invalid env kind."""
     with pytest.raises(ValueError, match="Invalid value for `env.kind`"):
         GnuParallelLocalAdapter(
-            job_name="check_env",
+            job_name="check_env_kind",
             job_dir=Path("."),
             yaml_config_path=Path("."),
             elements=["sub01"],
@@ -24,6 +24,18 @@ def test_GnuParallelLocalAdapter_env_error() -> None:
         )
 
 
+def test_GnuParallelLocalAdapter_env_shell_error() -> None:
+    """Test error for invalid env shell."""
+    with pytest.raises(ValueError, match="Invalid value for `env.shell`"):
+        GnuParallelLocalAdapter(
+            job_name="check_env_shell",
+            job_dir=Path("."),
+            yaml_config_path=Path("."),
+            elements=["sub01"],
+            env={"kind": "conda", "shell": "fish"},
+        )
+
+
 @pytest.mark.parametrize(
     "elements, expected_text",
     [
@@ -55,14 +67,18 @@ def test_GnuParallelLocalAdapter_elements(
 
 
 @pytest.mark.parametrize(
-    "pre_run, expected_text",
+    "pre_run, expected_text, shell",
     [
-        (None, "# Force datalad"),
-        ("# Check this out\n", "# Check this out"),
+        (None, "# Force datalad", "bash"),
+        (None, "# Force datalad", "zsh"),
+        ("# Check this out\n", "# Check this out", "bash"),
+        ("# Check this out\n", "# Check this out", "zsh"),
     ],
 )
 def test_GnuParallelLocalAdapter_pre_run(
-    pre_run: Optional[str], expected_text: str
+    pre_run: Optional[str],
+    expected_text: str,
+    shell: str,
 ) -> None:
     """Test GnuParallelLocalAdapter pre_run().
 
@@ -72,6 +88,8 @@ def test_GnuParallelLocalAdapter_pre_run(
         The parametrized pre run text.
     expected_text : str
         The parametrized expected text.
+    shell : str
+        The parametrized expected shell.
 
     """
     adapter = GnuParallelLocalAdapter(
@@ -79,21 +97,26 @@ def test_GnuParallelLocalAdapter_pre_run(
         job_dir=Path("."),
         yaml_config_path=Path("."),
         elements=["sub01"],
+        env={"kind": "conda", "name": "junifer", "shell": shell},
         pre_run=pre_run,
     )
+    assert shell in adapter.pre_run()
     assert expected_text in adapter.pre_run()
 
 
 @pytest.mark.parametrize(
-    "pre_collect, expected_text",
+    "pre_collect, expected_text, shell",
     [
-        (None, "# This script"),
-        ("# Check this out\n", "# Check this out"),
+        (None, "# This script", "bash"),
+        (None, "# This script", "zsh"),
+        ("# Check this out\n", "# Check this out", "bash"),
+        ("# Check this out\n", "# Check this out", "zsh"),
     ],
 )
 def test_GnuParallelLocalAdapter_pre_collect(
     pre_collect: Optional[str],
     expected_text: str,
+    shell: str,
 ) -> None:
     """Test GnuParallelLocalAdapter pre_collect().
 
@@ -103,6 +126,8 @@ def test_GnuParallelLocalAdapter_pre_collect(
         The parametrized pre collect text.
     expected_text : str
         The parametrized expected text.
+    shell : str
+        The parametrized expected shell.
 
     """
     adapter = GnuParallelLocalAdapter(
@@ -110,8 +135,10 @@ def test_GnuParallelLocalAdapter_pre_collect(
         job_dir=Path("."),
         yaml_config_path=Path("."),
         elements=["sub01"],
+        env={"kind": "venv", "name": "junifer", "shell": shell},
         pre_collect=pre_collect,
     )
+    assert shell in adapter.pre_collect()
     assert expected_text in adapter.pre_collect()
 
 
@@ -140,8 +167,10 @@ def test_GnuParallelLocalAdapter_collect() -> None:
 @pytest.mark.parametrize(
     "env",
     [
-        {"kind": "conda", "name": "junifer"},
-        {"kind": "venv", "name": "./junifer"},
+        {"kind": "conda", "name": "junifer", "shell": "bash"},
+        {"kind": "conda", "name": "junifer", "shell": "zsh"},
+        {"kind": "venv", "name": "./junifer", "shell": "bash"},
+        {"kind": "venv", "name": "./junifer", "shell": "zsh"},
     ],
 )
 def test_GnuParallelLocalAdapter_prepare(
@@ -177,7 +206,7 @@ def test_GnuParallelLocalAdapter_prepare(
             adapter.prepare()
 
             assert "GNU parallel" in caplog.text
-            assert f"Copying run_{env['kind']}" in caplog.text
+            assert f"Copying run_{env['kind']}.{env['shell']}" in caplog.text
             assert "Writing pre_run.sh" in caplog.text
             assert "Writing run_test_prepare.sh" in caplog.text
             assert "Writing pre_collect.sh" in caplog.text

junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -12,11 +12,11 @@ import pytest
 from junifer.api.queue_context import HTCondorAdapter
 
 
-def test_HTCondorAdapter_env_error() -> None:
+def test_HTCondorAdapter_env_kind_error() -> None:
     """Test error for invalid env kind."""
     with pytest.raises(ValueError, match="Invalid value for `env.kind`"):
         HTCondorAdapter(
-            job_name="check_env",
+            job_name="check_env_kind",
             job_dir=Path("."),
             yaml_config_path=Path("."),
             elements=["sub01"],
@@ -24,6 +24,18 @@ def test_HTCondorAdapter_env_error() -> None:
         )
 
 
+def test_HTCondorAdapter_env_shell_error() -> None:
+    """Test error for invalid env shell."""
+    with pytest.raises(ValueError, match="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="Invalid value for `collect`"):
@@ -37,14 +49,18 @@ def test_HTCondorAdapter_collect_error() -> None:
 
 
 @pytest.mark.parametrize(
-    "pre_run, expected_text",
+    "pre_run, expected_text, shell",
     [
-        (None, "# Force datalad"),
-        ("# Check this out\n", "# Check this out"),
+        (None, "# Force datalad", "bash"),
+        (None, "# Force datalad", "zsh"),
+        ("# Check this out\n", "# Check this out", "bash"),
+        ("# Check this out\n", "# Check this out", "zsh"),
     ],
 )
 def test_HTCondorAdapter_pre_run(
-    pre_run: Optional[str], expected_text: str
+    pre_run: Optional[str],
+    expected_text: str,
+    shell: str,
 ) -> None:
     """Test HTCondorAdapter pre_run().
 
@@ -54,6 +70,8 @@ def test_HTCondorAdapter_pre_run(
         The parametrized pre run text.
     expected_text : str
         The parametrized expected text.
+    shell : str
+        The parametrized expected shell.
 
     """
     adapter = HTCondorAdapter(
@@ -61,22 +79,31 @@ def test_HTCondorAdapter_pre_run(
         job_dir=Path("."),
         yaml_config_path=Path("."),
         elements=["sub01"],
+        env={"kind": "conda", "name": "junifer", "shell": shell},
         pre_run=pre_run,
     )
+    assert shell in adapter.pre_run()
     assert expected_text in adapter.pre_run()
 
 
 @pytest.mark.parametrize(
-    "pre_collect, expected_text, collect",
+    "pre_collect, expected_text, collect, shell",
     [
-        (None, "exit 1", "yes"),
-        (None, "# This script", "on_success_only"),
-        ("# Check this out\n", "# Check this out", "yes"),
-        ("# Check this out\n", "# Check this out", "on_success_only"),
+        (None, "exit 1", "yes", "bash"),
+        (None, "exit 1", "yes", "zsh"),
+        (None, "# This script", "on_success_only", "bash"),
+        (None, "# This script", "on_success_only", "zsh"),
+        ("# Check this out\n", "# Check this out", "yes", "bash"),
+        ("# Check this out\n", "# Check this out", "yes", "zsh"),
+        ("# Check this out\n", "# Check this out", "on_success_only", "bash"),
+        ("# Check this out\n", "# Check this out", "on_success_only", "zsh"),
     ],
 )
 def test_HTCondorAdapter_pre_collect(
-    pre_collect: Optional[str], expected_text: str, collect: str
+    pre_collect: Optional[str],
+    expected_text: str,
+    collect: str,
+    shell: str,
 ) -> None:
     """Test HTCondorAdapter pre_collect().
 
@@ -88,6 +115,8 @@ def test_HTCondorAdapter_pre_collect(
         The parametrized expected text.
     collect : str
         The parametrized collect parameter.
+    shell : str
+        The parametrized expected shell.
 
     """
     adapter = HTCondorAdapter(
@@ -95,9 +124,11 @@ def test_HTCondorAdapter_pre_collect(
         job_dir=Path("."),
         yaml_config_path=Path("."),
         elements=["sub01"],
+        env={"kind": "venv", "name": "junifer", "shell": shell},
         pre_collect=pre_collect,
         collect=collect,
     )
+    assert shell in adapter.pre_collect()
     assert expected_text in adapter.pre_collect()
 
 
@@ -177,8 +208,10 @@ def test_HTCondor_dag(
 @pytest.mark.parametrize(
     "env",
     [
-        {"kind": "conda", "name": "junifer"},
-        {"kind": "venv", "name": "./junifer"},
+        {"kind": "conda", "name": "junifer", "shell": "bash"},
+        {"kind": "conda", "name": "junifer", "shell": "zsh"},
+        {"kind": "venv", "name": "./junifer", "shell": "bash"},
+        {"kind": "venv", "name": "./junifer", "shell": "zsh"},
     ],
 )
 def test_HTCondorAdapter_prepare(
@@ -215,7 +248,7 @@ def test_HTCondorAdapter_prepare(
 
             assert "Creating HTCondor job" in caplog.text
             assert "Creating logs directory" in caplog.text
-            assert f"Copying run_{env['kind']}" in caplog.text
+            assert f"Copying run_{env['kind']}.{env['shell']}" in caplog.text
             assert "Writing pre_run.sh" in caplog.text
             assert "Writing run_test_prepare.submit" in caplog.text
             assert "Writing pre_collect.sh" in caplog.text

junifer/api/res/run_conda.bash

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 if [ $# -lt 2 ]; then
     echo "This script is meant to run a command within a conda environment."

junifer/api/res/run_conda.zsh

@@ -0,0 +1,23 @@
+#!/usr/bin/env zsh
+
+if [ $# -lt 2 ]; then
+    echo "This script is meant to run a command within a conda environment."
+    echo "It needs at least 2 parameters."
+    echo "The first one must be the environment name."
+    echo "The rest will be the command."
+    exit 255
+fi
+
+eval "$(conda shell.zsh hook)"
+env_name=$1
+echo "Activating ${env_name}"
+conda activate "${env_name}"
+shift 1
+
+if [ -f "pre_run.sh" ]; then
+    echo "Sourcing pre_run.sh"
+    . ./pre_run.sh
+fi
+
+echo "Running ${*} in conda environment"
+"$@"

junifer/api/res/run_venv.bash

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+if [ $# -lt 2 ]; then
+    echo "This script is meant to run a command within a Python virtual environment."
+    echo "It needs at least 2 parameters."
+    echo "The first one must be the virtualenv path."
+    echo "The rest will be the command."
+    exit 255
+fi
+
+env_path=$1
+echo "Activating ${env_path}"
+source "${env_path}"/bin/activate
+shift 1
+
+if [ -f "pre_run.sh" ]; then
+    echo "Sourcing pre_run.sh"
+    . ./pre_run.sh
+fi
+
+echo "Running ${*} in Python virtual environment"
+"$@"

junifer/api/res/run_venv.zsh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env zsh
 
 if [ $# -lt 2 ]; then
     echo "This script is meant to run a command within a Python virtual environment."

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -32,9 +32,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
         replacements = ["subject"]
         patterns = {
             "VBM_GM": {
-                "pattern": (
-                    "{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"
-                ),
+                "pattern": ("{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"),
                 "space": "IXI549Space",
             },
         }

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -44,9 +44,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
         replacements = ["site", "subject"]
         patterns = {
             "VBM_GM": {
-                "pattern": (
-                    "{site}/{subject}/mri/m0wp1{subject}.nii.gz"
-                ),
+                "pattern": ("{site}/{subject}/mri/m0wp1{subject}.nii.gz"),
                 "space": "IXI549Space",
             },
         }

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -33,8 +33,7 @@ def test_DataladAOMICID1000() -> None:
         assert "BOLD" in out
 
         assert (
-            out["BOLD"]["path"].name
-            == f"{test_element}_task-moviewatching_"
+            out["BOLD"]["path"].name == f"{test_element}_task-moviewatching_"
             "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
         )