junifer 0.0.5.dev164__tar.gz → 0.0.5.dev183__tar.gz

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/.github/workflows/ci.yml

@@ -66,36 +66,43 @@ jobs:
         sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni
         echo "/afni" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
+      # Bypass AFNI installation failure
+      continue-on-error: true
     - name: Check AFNI
       run: |
         echo "Using AFNI : $(afni --version)"
       if: matrix.python-version == 3.11
+      # Bypass AFNI installation failure
+      continue-on-error: true
     - name: Install ANTs
       run: |
         sudo apt-get install -y -qq unzip
-        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.2/ants-2.5.2-ubuntu-22.04-X64-gcc.zip
         unzip ants.zip -d /opt
-        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        mv /opt/ants-2.5.2/bin/* /opt/ants-2.5.2
         rm ants.zip
-        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
+        echo "/opt/ants-2.5.2" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
+      # Bypass ANTs installation failure
+      continue-on-error: true
     - name: Check ANTs
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
       if: matrix.python-version == 3.11
+      # Bypass ANTs installation failure
+      continue-on-error: true
     - name: Install FSL
       run: |
-        sudo apt-get install -y -qq python3
-        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.6.4 -V 6.0.6.4
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/
         FSLOUTPUTTYPE="NIFTI_GZ"
         FSLMULTIFILEQUIT="TRUE"
-        FSLTCLSH="/opt/fsl-6.0.6.4/bin/fsltclsh"
-        FSLWISH="/opt/fsl-6.0.6.4/bin/fslwish"
+        FSLTCLSH="/opt/fsl/bin/fsltclsh"
+        FSLWISH="/opt/fsl/bin/fslwish"
         FSLLOCKDIR=""
         FSLMACHINELIST=""
         FSLREMOTECALL=""
         FSLGECUDAQ="cuda.q"
-        echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
+        echo "/opt/fsl" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev164
+Version: 0.0.5.dev183
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -42,7 +42,7 @@ Requires-Dist: httpx[http2]==0.26.0
 Requires-Dist: tqdm==4.66.1
 Requires-Dist: templateflow>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
-Requires-Dist: importlib_metadata; python_version < "3.10"
+Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"

junifer-0.0.5.dev183/docs/changes/newsfragments/318.misc

@@ -0,0 +1 @@
+Improve CI to allow external tool installation to fail gracefully and update necessary dependency version and conditional checks by `Synchon Mandal`_

junifer-0.0.5.dev183/docs/changes/newsfragments/350.enh

@@ -0,0 +1 @@
+Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev164'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev164')
+__version__ = version = '0.0.5.dev183'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev183')

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/api/tests/test_api_utils.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 import platform as pl
+import sys
 
 import pytest
 
@@ -49,8 +50,7 @@ def test_get_dependency_information_short() -> None:
         "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(

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/data/masks.py

@@ -163,6 +163,10 @@ _available_masks: Dict[str, Dict[str, Any]] = {
         "func": compute_epi_mask,
         "space": "inherit",
     },
+    "UKB_15K_GM": {
+        "family": "UKB",
+        "space": "MNI152NLin6Asym",
+    },
 }
 
 
@@ -567,6 +571,8 @@ def load_mask(
     elif t_family == "Callable":
         mask_img = mask_definition["func"]
         mask_fname = None
+    elif t_family == "UKB":
+        mask_fname = _load_ukb_mask(name)
     else:
         raise_error(f"I don't know about the {t_family} mask family.")
 
@@ -632,3 +638,33 @@ def _load_vickery_patil_mask(
     mask_fname = _masks_path / "vickery-patil" / mask_fname
 
     return mask_fname
+
+
+def _load_ukb_mask(name: str) -> Path:
+    """Load UKB mask.
+
+    Parameters
+    ----------
+    name : {"UKB_15K_GM"}
+        The name of the mask.
+
+    Returns
+    -------
+    pathlib.Path
+        File path to the mask image.
+
+    Raises
+    ------
+    ValueError
+        If ``name`` is invalid.
+
+    """
+    if name == "UKB_15K_GM":
+        mask_fname = "UKB_15K_GM_template.nii.gz"
+    else:
+        raise_error(f"Cannot find a UKB mask called {name}")
+
+    # Set path for masks
+    mask_fname = _masks_path / "ukb" / mask_fname
+
+    return mask_fname

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/data/tests/test_masks.py

@@ -22,6 +22,7 @@ from numpy.testing import assert_array_almost_equal, assert_array_equal
 
 from junifer.data.masks import (
     _available_masks,
+    _load_ukb_mask,
     _load_vickery_patil_mask,
     compute_brain_mask,
     get_mask,
@@ -212,6 +213,7 @@ def test_register_mask(
     [
         "GM_prob0.2",
         "GM_prob0.2_cortex",
+        "UKB_15K_GM",
     ],
 )
 def test_list_masks_correct(mask_name: str) -> None:
@@ -291,6 +293,21 @@ def test_vickery_patil_error() -> None:
         _load_vickery_patil_mask(name="wrong", resolution=2.0)
 
 
+def test_ukb() -> None:
+    """Test UKB mask."""
+    mask, mask_fname, space = load_mask("UKB_15K_GM", resolution=2.0)
+    assert_array_almost_equal(mask.header["pixdim"][1:4], 2.0)  # type: ignore
+    assert space == "MNI152NLin6Asym"
+    assert mask_fname is not None
+    assert mask_fname.name == "UKB_15K_GM_template.nii.gz"
+
+
+def test_ukb_error() -> None:
+    """Test error for UKB mask."""
+    with pytest.raises(ValueError, match=r"find a UKB mask "):
+        _load_ukb_mask(name="wrong")
+
+
 def test_get_mask() -> None:
     """Test the get_mask function."""
     with OasisVBMTestingDataGrabber() as dg:

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/markers/brainprint.py

@@ -3,10 +3,13 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-try:
-    from importlib.metadata import packages_distributions
-except ImportError:  # pragma: no cover
+import sys
+
+
+if sys.version_info < (3, 11):  # pragma: no cover
     from importlib_metadata import packages_distributions
+else:
+    from importlib.metadata import packages_distributions
 
 import uuid
 from copy import deepcopy

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/markers/falff/_afni_falff.py

@@ -124,7 +124,7 @@ class AFNIALFF:
         convert_alff_cmd = [
             "3dAFNItoNIFTI",
             f"-prefix {alff_afni_to_nifti_out_path.resolve()}",
-            f"{alff_falff_out_path_prefix}_ALFF+tlrc.BRIK",
+            f"{alff_falff_out_path_prefix}_ALFF+orig.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_alff_cmd)
@@ -136,7 +136,7 @@ class AFNIALFF:
         convert_falff_cmd = [
             "3dAFNItoNIFTI",
             f"-prefix {falff_afni_to_nifti_out_path.resolve()}",
-            f"{alff_falff_out_path_prefix}_fALFF+tlrc.BRIK",
+            f"{alff_falff_out_path_prefix}_fALFF+orig.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_falff_cmd)

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/markers/reho/_afni_reho.py

@@ -181,7 +181,7 @@ class AFNIReHo:
         convert_cmd = [
             "3dAFNItoNIFTI",
             f"-prefix {reho_afni_to_nifti_out_path.resolve()}",
-            f"{reho_out_path_prefix}+tlrc.BRIK",
+            f"{reho_out_path_prefix}+orig.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_cmd)

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/pipeline/pipeline_step_mixin.py

@@ -4,10 +4,14 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-try:
-    from importlib.metadata import packages_distributions
-except ImportError:  # pragma: no cover
+import sys
+
+
+if sys.version_info < (3, 11):  # pragma: no cover
     from importlib_metadata import packages_distributions
+else:
+    from importlib.metadata import packages_distributions
+
 
 from importlib.util import find_spec
 from itertools import chain

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/preprocess/smoothing/_afni_smoothing.py

@@ -105,7 +105,7 @@ class AFNISmoothing:
         convert_cmd = [
             "3dAFNItoNIFTI",
             f"-prefix {blur_afni_to_nifti_out_path.resolve()}",
-            f"{blur_out_path_prefix}+tlrc.BRIK",
+            f"{blur_out_path_prefix}+orig.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_cmd)

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer/utils/logging.py

@@ -4,13 +4,15 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-try:
+import sys
+
+
+if sys.version_info < (3, 12):
     from distutils.version import LooseVersion
-except ImportError:  # pragma: no cover
+else:  # pragma: no cover
     from looseversion import LooseVersion
 
 import logging
-import sys
 from pathlib import Path
 from subprocess import PIPE, Popen, TimeoutExpired
 from typing import Dict, NoReturn, Optional, Type, Union

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev164
+Version: 0.0.5.dev183
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -42,7 +42,7 @@ Requires-Dist: httpx[http2]==0.26.0
 Requires-Dist: tqdm==4.66.1
 Requires-Dist: templateflow>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
-Requires-Dist: importlib_metadata; python_version < "3.10"
+Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer.egg-info/SOURCES.txt

@@ -61,6 +61,7 @@ docs/changes/newsfragments/115.doc
 docs/changes/newsfragments/136.enh
 docs/changes/newsfragments/161.feature
 docs/changes/newsfragments/273.feature
+docs/changes/newsfragments/318.misc
 docs/changes/newsfragments/323.feature
 docs/changes/newsfragments/324.bugfix
 docs/changes/newsfragments/327.doc
@@ -79,6 +80,7 @@ docs/changes/newsfragments/345.feature
 docs/changes/newsfragments/346.enh
 docs/changes/newsfragments/346.feature
 docs/changes/newsfragments/347.misc
+docs/changes/newsfragments/350.enh
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -204,6 +206,7 @@ junifer/data/VOIs/meta/WM_VOIs.txt
 junifer/data/VOIs/meta/eMDN_VOIs.txt
 junifer/data/VOIs/meta/eSAD_VOIs.txt
 junifer/data/VOIs/meta/extDMN_VOIs.txt
+junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.nii.gz
 junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/junifer.egg-info/requires.txt

@@ -13,7 +13,7 @@ tqdm==4.66.1
 templateflow>=23.0.0
 lapy<2.0.0,>=1.0.0
 
-[:python_version < "3.10"]
+[:python_version < "3.9"]
 importlib_metadata
 
 [:python_version >= "3.12"]

{junifer-0.0.5.dev164 → junifer-0.0.5.dev183}/pyproject.toml

@@ -50,7 +50,7 @@ dependencies = [
     "tqdm==4.66.1",
     "templateflow>=23.0.0",
     "lapy>=1.0.0,<2.0.0",
-    "importlib_metadata; python_version<'3.10'",
+    "importlib_metadata; python_version<'3.9'",
     "looseversion==1.3.0; python_version>='3.12'",
 ]
 dynamic = ["version"]