junifer 0.0.5.dev161__tar.gz → 0.0.5.dev180__tar.gz

{junifer-0.0.5.dev161 → junifer-0.0.5.dev180}/.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.dev161 → junifer-0.0.5.dev180}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev161
+Version: 0.0.5.dev180
 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.dev180/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.dev180/docs/changes/newsfragments/327.doc

@@ -0,0 +1 @@
+Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_

{junifer-0.0.5.dev161 → junifer-0.0.5.dev180}/docs/using/queueing.rst

@@ -10,10 +10,10 @@ computational clusters. This is done by adding the ``queue`` section in the
 :ref:`codeless` file and executing the  ``junifer queue`` command.
 
 While junifer is meant to support `HTCondor`_, `SLURM`_ and local queueing
-using `GNU Parallel`_, only HTCondor is currently supported. This will be
-implemented in future releases of ``junifer``. If you are in immediate need of
-any of these schedulers, please create an issue on the `junifer github`_
-repository.
+using `GNU Parallel`_, only ``HTCondor`` and ``GNU Parallel`` are currently
+supported. This will be implemented in future releases of ``junifer``. If you are
+in immediate need of any of these schedulers, please create an issue on the
+`junifer github`_ repository.
 
 The ``queue`` section of the :ref:`codeless` must start by defining the
 following general parameters:
@@ -22,8 +22,8 @@ following general parameters:
   folder where the job files will be created, as well as any relevant file.
   Depending on the scheduler, it will also be listed in the queueing system
   with this name.
-* ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` is
-  supported.
+* ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` and
+  ``GNUParallelLocal`` are supported.
 
 Example in YAML:
 
@@ -48,7 +48,9 @@ jobs are finished.
 
 The following parameters are available for HTCondor:
 
-* ``env``: Definition of the Python environment. It must provide two variables:
+* ``pre_run``: Extra shell commands to run before ``junifer run``.
+* ``pre_collect``: Extra shell commands to run before ``junifer collect``.
+* ``env``: Definition of the Python environment. It has the following parameters:
 
   * ``kind``: This is the kind of virtual environment to use:
 
@@ -61,6 +63,9 @@ The following parameters are available for HTCondor:
     the absolute or relative path to the virtualenv when ``venv`` is used.
     If relative path is used then it should be relative to the YAML.
 
+  * ``shell``: This is the shell to use. Only ``bash`` and ``zsh`` are supported
+    as of now.
+
 * ``mem``: Memory to be used by the job. It must be provided as a string with
   the units (e.g., ``"2GB"``).
 * ``cpus``: Number of CPUs to be used by the job. It must be provided as an
@@ -93,10 +98,78 @@ Example in YAML:
     env:
       kind: conda
       name: junifer
+      shell: zsh
+    mem: 8G
+    disk: 2G
+    collect: "yes"  # wrap it in string to avoid boolean
+
+Alternatively, if you use ``venv``, the YAML would look like so:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestHTCondorQueue
+    kind: HTCondor
+    env:
+      kind: venv
+      name: /home/me/junifer-venv  # should be at the level above `bin/activate`
+      shell: zsh
     mem: 8G
     disk: 2G
     collect: "yes"  # wrap it in string to avoid boolean
 
+.. _queueing_local:
+
+GNUParallelLocal
+----------------
+
+When using GNU Parallel, ``junifer`` will run only in local mode and leverage
+maximum computational power of whatever hardware it is run on.
+
+The following parameters are available for GNUParallelLocal:
+
+* ``pre_run``: Extra shell commands to run before ``junifer run``.
+* ``pre_collect``: Extra shell commands to run before ``junifer collect``.
+* ``env``: Definition of the Python environment. It has the following parameters:
+
+  * ``kind``: This is the kind of virtual environment to use:
+
+    * ``conda``
+    * ``venv``
+    * ``local`` (no virtual environment)
+
+  * ``name``: This is the name of the environment to use in case a virtual
+    environment is used. It should be the name when ``conda`` is used and
+    the absolute or relative path to the virtualenv when ``venv`` is used.
+    If relative path is used then it should be relative to the YAML.
+
+  * ``shell``: This is the shell to use. Only ``bash`` and ``zsh`` are supported
+    as of now.
+
+Example in YAML:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestGNUParallelLocalQueue
+    kind: GNUParallelLocal
+    env:
+      kind: conda
+      name: junifer
+      shell: zsh
+
+Alternatively, if you use ``venv``, the YAML would look like so:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestGNUParallelLocalQueue
+    kind: GNUParallelLocal
+    env:
+      kind: venv
+      name: /home/me/junifer-venv  # should be at the level above `bin/activate`
+      shell: zsh
+
 Once the :ref:`codeless` file is ready, including the ``queue`` section, you can
 queue the jobs by executing the ``junifer queue`` command.
 

{junifer-0.0.5.dev161 → junifer-0.0.5.dev180}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev161'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev161')
+__version__ = version = '0.0.5.dev180'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev180')

{junifer-0.0.5.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev161
+Version: 0.0.5.dev180
 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.dev161 → junifer-0.0.5.dev180}/junifer.egg-info/SOURCES.txt

@@ -61,8 +61,10 @@ 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
 docs/changes/newsfragments/330.doc
 docs/changes/newsfragments/331.bugfix
 docs/changes/newsfragments/332.bugfix

{junifer-0.0.5.dev161 → junifer-0.0.5.dev180}/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.dev161 → junifer-0.0.5.dev180}/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"]