junifer 0.0.4.dev829__py3-none-any.whl → 0.0.5__py3-none-any.whl

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/afni/run_afni_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for afni: ${corrected_args[*]}" >&2
+echo "Corrected args for AFNI: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}"

junifer/api/res/ants/run_ants_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for fsl: ${corrected_args[*]}" >&2
+echo "Corrected args for ANTs: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} antsx/ants ${corrected_args[*]}"

junifer/api/res/freesurfer/mri_binarize

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mri_binarize "$@"

junifer/api/res/freesurfer/mri_mc

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mri_mc "$@"

junifer/api/res/freesurfer/mri_pretess

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mri_pretess "$@"

junifer/api/res/freesurfer/mris_convert

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mris_convert "$@"

junifer/api/res/freesurfer/run_freesurfer_docker.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+
+corrected_args=()
+docker_args=()
+mounts=0
+
+FS_LICENSE="${FS_LICENSE:=$HOME/freesurfer_license.txt}"
+
+if [ -f "${FS_LICENSE}" ]; then
+    >&2 echo "Using freesurfer license from ${FS_LICENSE}"
+else
+    >&2 echo "Freesurfer license not found at ${FS_LICENSE}. You can either set FS_LICENSE to the path of the license file or place the license file at
+${FS_LICENSE}"
+    exit 1
+fi
+
+# Map the license path to the container by binding
+license_path=$(realpath "${FS_LICENSE}")
+license_path_fname=$(basename "${FS_LICENSE}")
+host_dir=$(dirname "${license_path}")
+((mounts+=1))
+container_dir="/data/mount_${mounts}"
+docker_args+=("-v ${host_dir}:${container_dir}")
+export DOCKERENV_FS_LICENSE=${container_dir}/${license_path_fname}
+
+for var in "$@"
+do
+if [ -d "${var}" ]; then
+        echo "$var is a directory" >&2
+        var=$(realpath "${var}")
+        host_dir=$(dirname "${var}")
+        ((mounts+=1))
+        container_dir="/data/mount_${mounts}"
+        docker_args+=("-v ${host_dir}:${container_dir}")
+        var=${container_dir}
+    elif [ -f "${var}" ] || [[ "${var}" == /* ]]; then
+        if [ -f "${var}" ]; then
+            echo "$var is a file" >&2
+            var=$(realpath "${var}")
+        else
+            echo "$var is a prefix" >&2
+        fi
+        fname=$(basename "${var}")
+        host_dir=$(dirname "${var}")
+        ((mounts+=1))
+        container_dir="/data/mount_${mounts}"
+        docker_args+=("-v ${host_dir}:${container_dir}")
+        var=${container_dir}/${fname}
+    fi
+    corrected_args+=("${var}")
+done
+
+echo "Docker args: ${docker_args[*]}" >&2
+echo "Corrected args for FreeSurfer: ${corrected_args[*]}" >&2
+
+cwd=$(pwd)
+cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} freesurfer/freesurfer ${corrected_args[*]}"
+echo "Running command: ${cmd}" >&2
+${cmd}
+
+unset DOCKERENV_FS_LICENSE

junifer/api/res/fsl/run_fsl_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for fsl: ${corrected_args[*]}" >&2
+echo "Corrected args for FSL: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"

junifer/api/res/{run_conda.sh → 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.sh → 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/api/tests/test_api_utils.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 import platform as pl
+import sys
 
 import pytest
 
@@ -45,11 +46,11 @@ def test_get_dependency_information_short() -> None:
         "httpx",
         "tqdm",
         "templateflow",
+        "lapy",
         "looseversion",
     ]
 
-    python_minor_version = int(pl.python_version_tuple()[1])
-    if python_minor_version < 10:
+    if sys.version_info < (3, 11):
         dependency_list.append("importlib_metadata")
 
     assert frozenset(dependency_information.keys()) == frozenset(
@@ -74,6 +75,7 @@ def test_get_dependency_information_long() -> None:
         "httpx",
         "tqdm",
         "templateflow",
+        "lapy",
     ]
     for key in dependency_list:
         assert key in dependency_information_keys

junifer/api/tests/test_cli.py

@@ -14,6 +14,7 @@ from ruamel.yaml import YAML
 from junifer.api.cli import (
     _parse_elements_file,
     collect,
+    list_elements,
     queue,
     reset,
     run,
@@ -297,6 +298,88 @@ def test_reset(
         assert reset_result.exit_code == 0
 
 
+@pytest.mark.parametrize(
+    "elements",
+    [
+        ("sub-01", "sub-02"),
+        ("sub-03", "sub-04"),
+    ],
+)
+def test_list_elements_stdout(
+    elements: Tuple[str, ...],
+) -> None:
+    """Test elements listing to stdout.
+
+    Parameters
+    ----------
+    elements : tuple of str
+        The parametrized elements for filtering.
+
+    """
+    # Get test config
+    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
+    # List elements command arguments
+    list_elements_args = [
+        str(infile.absolute()),
+        "--verbose",
+        "debug",
+        "--element",
+        elements[0],
+        "--element",
+        elements[1],
+    ]
+    # Invoke list elements command
+    list_elements_result = runner.invoke(list_elements, list_elements_args)
+    # Check
+    assert list_elements_result.exit_code == 0
+    assert f"{elements[0]}\n{elements[1]}" in list_elements_result.stdout
+
+
+@pytest.mark.parametrize(
+    "elements",
+    [
+        ("sub-01", "sub-02"),
+        ("sub-03", "sub-04"),
+    ],
+)
+def test_list_elements_output_file(
+    tmp_path: Path,
+    elements: Tuple[str, ...],
+) -> None:
+    """Test elements listing to output file.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+    elements : tuple of str
+        The parametrized elements for filtering.
+
+    """
+    # Get test config
+    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
+    # Output file
+    output_file = tmp_path / "elements.txt"
+    # List elements command arguments
+    list_elements_args = [
+        str(infile.absolute()),
+        "--verbose",
+        "debug",
+        "--element",
+        elements[0],
+        "--element",
+        elements[1],
+        "--output-file",
+        str(output_file.resolve()),
+    ]
+    # Invoke list elements command
+    list_elements_result = runner.invoke(list_elements, list_elements_args)
+    # Check
+    assert list_elements_result.exit_code == 0
+    with open(output_file) as f:
+        assert f"{elements[0]}\n{elements[1]}" == f.read()
+
+
 def test_wtf_short() -> None:
     """Test short version of wtf command."""
     # Invoke wtf command

junifer/api/tests/test_functions.py

@@ -7,13 +7,13 @@
 
 import logging
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import pytest
 from ruamel.yaml import YAML
 
 import junifer.testing.registry  # noqa: F401
-from junifer.api.functions import collect, queue, reset, run
+from junifer.api.functions import collect, list_elements, queue, reset, run
 from junifer.datagrabber.base import BaseDataGrabber
 from junifer.pipeline.registry import build
 
@@ -637,3 +637,28 @@ def test_reset_queue(
 
         assert not Path(storage["uri"]).exists()
         assert not (tmp_path / "junifer_jobs" / job_name).exists()
+
+
+@pytest.mark.parametrize(
+    "elements",
+    [
+        ["sub-01"],
+        None,
+    ],
+)
+def test_list_elements(
+    datagrabber: Dict[str, str],
+    elements: Optional[List[str]],
+) -> None:
+    """Test elements listing.
+
+    Parameters
+    ----------
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    elements : str of list of str
+        The parametrized elements for filtering.
+
+    """
+    listed_elements = list_elements(datagrabber, elements)
+    assert "sub-01" in listed_elements

junifer/configs/__init__.py

@@ -1,4 +1,4 @@
-"""Provide imports for configs sub-package."""
+"""Custom components for specific platforms."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL

junifer/configs/juseless/__init__.py

@@ -1,6 +1,9 @@
-"""Provide imports for juseless sub-package."""
+"""Custom components for FZJ INM-7's beloved juseless."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
 from . import datagrabbers
+
+
+__all__ = ["datagrabbers"]

junifer/configs/juseless/datagrabbers/__init__.py

@@ -1,4 +1,4 @@
-"""Provide imports for datagrabbers sub-package."""
+"""Custom DataGrabbers for FZJ INM-7's beloved juseless."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -10,3 +10,12 @@ from .camcan_vbm import JuselessDataladCamCANVBM
 from .ixi_vbm import JuselessDataladIXIVBM
 from .ucla import JuselessUCLA
 from .ukb_vbm import JuselessDataladUKBVBM
+
+
+__all__ = [
+    "JuselessDataladAOMICID1000VBM",
+    "JuselessDataladCamCANVBM",
+    "JuselessDataladIXIVBM",
+    "JuselessUCLA",
+    "JuselessDataladUKBVBM",
+]

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -11,6 +11,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladAOMICID1000VBM"]
+
+
 @register_datagrabber
 class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.
@@ -32,9 +35,7 @@ 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/camcan_vbm.py

@@ -12,6 +12,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladCamCANVBM"]
+
+
 @register_datagrabber
 class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless CamCAN VBM data fetching.

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -13,6 +13,9 @@ from ....datagrabber import PatternDataladDataGrabber
 from ....utils import raise_error
 
 
+__all__ = ["JuselessDataladIXIVBM"]
+
+
 @register_datagrabber
 class JuselessDataladIXIVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless IXI VBM data fetching.
@@ -44,9 +47,7 @@ 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/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -27,7 +27,6 @@ def test_JuselessUCLA() -> None:
 
         types = [
             "BOLD",
-            "BOLD_confounds",
             "T1w",
             "VBM_CSF",
             "VBM_GM",
@@ -43,12 +42,11 @@ def test_JuselessUCLA() -> None:
     "types",
     [
         "BOLD",
-        "BOLD_confounds",
         "T1w",
         "VBM_CSF",
         "VBM_GM",
         "VBM_WM",
-        ["BOLD", "BOLD_confounds"],
+        ["BOLD", "VBM_CSF"],
         ["T1w", "VBM_CSF"],
         ["VBM_GM", "VBM_WM"],
         ["BOLD", "T1w"],

junifer/configs/juseless/datagrabbers/ucla.py

@@ -12,6 +12,9 @@ from ....datagrabber import PatternDataGrabber
 from ....utils import raise_error
 
 
+__all__ = ["JuselessUCLA"]
+
+
 @register_datagrabber
 class JuselessUCLA(PatternDataGrabber):
     """Concrete implementation for Juseless UCLA data fetching.
@@ -23,8 +26,8 @@ class JuselessUCLA(PatternDataGrabber):
     datadir : str or Path, optional
         The directory where the dataset is stored.
         (default "/data/project/psychosis_thalamus/data/fmriprep").
-    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
-           "VBM_WM"} or a list of the options, optional
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM"} or \
+           list of the options, optional
         UCLA data types. If None, all available data types are selected.
         (default None).
     tasks : {"rest", "bart", "bht", "pamenc", "pamret", \
@@ -76,13 +79,13 @@ class JuselessUCLA(PatternDataGrabber):
                     "MNI152NLin2009cAsym_preproc.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-            },
-            "BOLD_confounds": {
-                "pattern": (
-                    "{subject}/func/{subject}_"
-                    "task-{task}_bold_confounds.tsv"
-                ),
-                "space": "fmriprep",
+                "confounds": {
+                    "pattern": (
+                        "{subject}/func/{subject}_"
+                        "task-{task}_bold_confounds.tsv"
+                    ),
+                    "space": "fmriprep",
+                },
             },
             "T1w": {
                 "pattern": (

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -12,6 +12,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladUKBVBM"]
+
+
 @register_datagrabber
 class JuselessDataladUKBVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless UKB VBM data fetching.