Merge pull request #318 from juaml/chore/fix-ci

[CI]: Improve CI

.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

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/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/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/markers/falff/_afni_falff.py

@@ -124,7 +124,7 @@ def compute(
         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 @@ def compute(
         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/markers/reho/_afni_reho.py

@@ -181,7 +181,7 @@ def compute(
         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/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/preprocess/smoothing/_afni_smoothing.py

@@ -105,7 +105,7 @@ def preprocess(
         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/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

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"]