junifer 0.0.5__tar.gz → 0.0.5.dev24__tar.gz

{junifer-0.0.5 → junifer-0.0.5.dev24}/.github/workflows/ci.yml

@@ -66,43 +66,36 @@ 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/v2.5.2/ants-2.5.2-ubuntu-22.04-X64-gcc.zip
+        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
         unzip ants.zip -d /opt
-        mv /opt/ants-2.5.2/bin/* /opt/ants-2.5.2
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
         rm ants.zip
-        echo "/opt/ants-2.5.2" >> $GITHUB_PATH
+        echo "/opt/ants-2.5.1" >> $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: |
-        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/
+        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
         FSLOUTPUTTYPE="NIFTI_GZ"
         FSLMULTIFILEQUIT="TRUE"
-        FSLTCLSH="/opt/fsl/bin/fsltclsh"
-        FSLWISH="/opt/fsl/bin/fslwish"
+        FSLTCLSH="/opt/fsl-6.0.6.4/bin/fsltclsh"
+        FSLWISH="/opt/fsl-6.0.6.4/bin/fslwish"
         FSLLOCKDIR=""
         FSLMACHINELIST=""
         FSLREMOTECALL=""
         FSLGECUDAQ="cuda.q"
-        echo "/opt/fsl" >> $GITHUB_PATH
+        echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true

{junifer-0.0.5 → junifer-0.0.5.dev24}/.github/workflows/docs.yml

@@ -68,7 +68,7 @@ jobs:
         touch docs/_build/.nojekyll
         cp docs/redirect.html docs/_build/index.html
     - name: Publish docs to gh-pages
-      uses: peaceiris/actions-gh-pages@v4
+      uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/_build

junifer-0.0.5.dev24/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "junifer/external/h5io"]
+	path = junifer/external/h5io
+	url = https://github.com/juaml/h5io

{junifer-0.0.5 → junifer-0.0.5.dev24}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-docstring-first
@@ -20,14 +20,14 @@ repos:
     rev: v0.16
     hooks:
       - id: validate-pyproject
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.2
+    rev: v0.1.15
     hooks:
       - id: ruff
         types_or: [python, jupyter]
@@ -38,7 +38,7 @@ repos:
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
-        args: [--toml, pyproject.toml]
+        args: [--config, tox.ini]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
@@ -47,10 +47,3 @@ repos:
       - id: rst-backticks
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
-  - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
-    hooks:
-      - id: blacken-docs
-        additional_dependencies:
-          - black==24.4.2
-        args: [-l 79]

{junifer-0.0.5 → junifer-0.0.5.dev24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5
+Version: 0.0.5.dev24
 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>
@@ -29,20 +29,19 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<2.0.0,>=1.24.0
-Requires-Dist: scipy<=1.14.0,>=1.10.0
-Requires-Dist: datalad<1.2.0,>=1.0.0
-Requires-Dist: pandas<2.3.0,>=2.0.0
-Requires-Dist: nibabel<5.3.0,>=5.2.0
-Requires-Dist: nilearn<=0.10.4,>=0.10.3
-Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
+Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: scipy<=1.11.4,>=1.9.0
+Requires-Dist: datalad<0.20,>=0.15.4
+Requires-Dist: pandas<2.2,>=1.4.0
+Requires-Dist: nibabel<5.11,>=3.2.0
+Requires-Dist: nilearn<=0.10.2,>=0.9.0
+Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
 Requires-Dist: ruamel.yaml<0.18,>=0.17
 Requires-Dist: h5py>=3.10
 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 < "3.9"
+Requires-Dist: importlib_metadata; python_version < "3.10"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
@@ -57,14 +56,14 @@ Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
-Requires-Dist: sphinx<7.4.0,>=7.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<0.17.0,>=0.15.0; extra == "docs"
-Requires-Dist: furo<2024.6.0,>=2024.4.27; extra == "docs"
-Requires-Dist: numpydoc<1.8.0,>=1.6.0; extra == "docs"
-Requires-Dist: julearn==0.3.3; extra == "docs"
+Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
+Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
+Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
+Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
+Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<23.12.0,>=23.10.0; extra == "docs"
+Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")

{junifer-0.0.5 → junifer-0.0.5.dev24}/docs/api/nilearn.rst

@@ -1,6 +1,8 @@
 Nilearn
 =======
 
+This package provides re-implementations of some of the functions in `nilearn`_.
+
 .. automodule:: junifer.external.nilearn
    :members:
    :imported-members:

{junifer-0.0.5 → junifer-0.0.5.dev24}/docs/api/onthefly.rst

@@ -1,6 +1,8 @@
 On-the-fly
 ==========
 
+This package provides functions for quick transform operations on stored data.
+
 .. automodule:: junifer.onthefly
    :members:
    :imported-members:

{junifer-0.0.5 → junifer-0.0.5.dev24}/docs/builtin.rst

@@ -729,6 +729,14 @@ Available
      - | Compute a brain mask for the images by guessing the value of the
        | background from the border of the image.
        | See :func:`nilearn.masking.compute_background_mask`
+   * - ``nilearn``'s ICBM152 template gray-matter mask
+     - | ``fetch_icbm152_brain_gm_mask``
+     - ``MNI152NLin2009aAsym``
+     - 0.0.2
+     - | Compute a gray-matter mask from the asymmetrical ICBM152 2009 template,
+       | release a.
+       | See :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`
+
 
 ..
    Planned

junifer-0.0.5.dev24/docs/changes/newsfragments/161.feature

@@ -0,0 +1 @@
+Introduce :class:`.Smoothing` for smoothing / blurring images as a preprocessing step by `Synchon Mandal`_

junifer-0.0.5.dev24/docs/changes/newsfragments/273.feature

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

{junifer-0.0.5 → junifer-0.0.5.dev24}/docs/conf.py

@@ -170,7 +170,6 @@ numpydoc_xref_ignore = {
     "Engine",
     "positive",
     "negative",
-    "estimator",
 }
 # numpydoc_validation_checks = {
 #     "all",

{junifer-0.0.5 → junifer-0.0.5.dev24}/docs/extending/coordinates.rst

@@ -70,7 +70,10 @@ with the DMN. Here, we use the DMN coordinates used in a
 .. code-block:: python
 
   dmn_coords = np.array(
-      [[0, -52, 18], [-46, -68, 32], [46, -68, 32], [1, 50, -5]]
+      [[0, -52, 18],
+      [-46, -68, 32],
+      [46, -68, 32],
+      [1, 50, -5]]
   )
   voi_names = [
       "Posterior Cingulate Cortex",
@@ -87,7 +90,10 @@ simply use this to register our coordinates:
 .. code-block:: python
 
   register_coordinates(
-      name="DMNCustom", coordinates=dmn_coords, voi_names=voi_names, space="MNI"
+      name="DMNCustom",
+      coordinates=dmn_coords,
+      voi_names=voi_names,
+      space="MNI"
   )
 
 Now, when we run this script, ``junifer`` registers these coordinates and we can