junifer 0.0.6.dev116__tar.gz → 0.0.6.dev142__tar.gz

junifer-0.0.6.dev142/.github/workflows/docs-preview.yml

@@ -0,0 +1,63 @@
+name: Build and preview docs
+
+on:
+  push:
+    branches-ignore:
+      - 'main'
+    tags-ignore:
+      - v*
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+concurrency: preview-${{ github.ref }}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    # Use custom docs CI image
+    container: ghcr.io/juaml/junifer-docs:main
+    steps:
+    - name: Check ANTs
+      run: |
+        echo "Using ANTs : $(antsRegistration --version)"
+    - name: Install system dependencies
+      run: |
+        # actions/checkout fails to identify Git as it's not in the CI image
+        apt-get -qq update && \
+        apt-get -qq install -y \
+        git \
+        git-annex \
+        make \
+        jq
+        # Copy xfms directory
+        mkdir -p $HOME/junifer/data/xfms && \
+        cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
+    - name: Checkout source
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install -e ".[docs,neurokit2]"
+    - name: Configure Git for DataLad
+      run: |
+        git config --global user.email "junifer-runner@github.com"
+        git config --global user.name "GitHub Runner"
+    - name: Test build docs
+      run: |
+        BUILDDIR=_build/main make -C docs/ local
+    - name: Deploy preview
+      if: github.event_name == 'pull_request'
+      uses: rossjrw/pr-preview-action@v1
+      with:
+        source-dir: docs/_build/main

{junifer-0.0.6.dev116 → junifer-0.0.6.dev142}/.github/workflows/docs.yml

@@ -12,7 +12,24 @@ on:
 jobs:
   build-docs:
     runs-on: ubuntu-latest
+    # Use custom docs CI image
+    container: ghcr.io/juaml/junifer-docs:main
     steps:
+    - name: Check ANTs
+      run: |
+        echo "Using ANTs : $(antsRegistration --version)"
+    - name: Install system dependencies
+      run: |
+        # actions/checkout fails to identify Git as it's not in the CI image
+        apt-get -qq update && \
+        apt-get -qq install -y \
+        git \
+        git-annex \
+        make \
+        jq
+        # Copy xfms directory
+        mkdir -p $HOME/junifer/data/xfms && \
+        cp -ar /root/junifer/data/xfms/. $HOME/junifer/data/xfms/
     - name: Checkout source
       uses: actions/checkout@v4
       with:
@@ -23,37 +40,15 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.x"
-    - name: Check for sudo
-      shell: bash
-      run: |
-        if type sudo >/dev/null 2>&1; then SUDO="sudo"; else SUDO=""; fi
-        echo "SUDO=$SUDO" >> $GITHUB_ENV
-    - name: Install dependencies
+    - name: Install Python dependencies
       run: |
-        $SUDO bash -c "$(curl -fsSL http://neuro.debian.net/_files/neurodebian-travis.sh)"
-        $SUDO apt-get update -qq
-        $SUDO apt-get install git-annex-standalone
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install -e ".[docs,neurokit2]"
         python -m pip install git+https://github.com/dls-controls/sphinx-multiversion@only-arg
-    - name: Configure git for datalad
+    - name: Configure Git for DataLad
       run: |
-        git config --global user.email "runner@github.com"
-        git config --global user.name "GITHUB CI Runner"
-    - name: Install ANTs
-      run: |
-        echo "++ Add universe repo"
-        sudo add-apt-repository -y universe
-
-        echo "++ Update package manager info"
-        sudo apt-get update -qq
-
-        echo "++ Downloading ANTs"
-        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-2.5.1/bin/* /opt/ants-2.5.1
-        rm ants.zip
-        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
+        git config --global user.email "junifer-runner@github.com"
+        git config --global user.name "GitHub Runner"
     - name: Checkout gh-pages
       # As we already did a deploy of gh-pages above, it is guaranteed to be there
       # so check it out so we can selectively build docs below

{junifer-0.0.6.dev116 → junifer-0.0.6.dev142}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev116
+Version: 0.0.6.dev142
 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>

junifer-0.0.6.dev142/docs/changes/newsfragments/368.enh

@@ -0,0 +1 @@
+Use ``datalad``-enabled repository for template space transform files in :func:`.get_xfm` by `Synchon Mandal`_

junifer-0.0.6.dev142/docs/changes/newsfragments/374.misc

@@ -0,0 +1 @@
+Adopt usage of custom docs CI image for building and previewing docs actions by `Synchon Mandal`_

{junifer-0.0.6.dev116 → junifer-0.0.6.dev142}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev116'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev116')
+__version__ = version = '0.0.6.dev142'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev142')

{junifer-0.0.6.dev116 → junifer-0.0.6.dev142}/junifer/data/template_spaces.py

@@ -6,9 +6,10 @@
 from pathlib import Path
 from typing import Any, Dict, Optional, Union
 
-import httpx
+import datalad.api as dl
 import nibabel as nib
 import numpy as np
+from datalad.support.exceptions import IncompleteResultsError
 from templateflow import api as tflow
 
 from ..utils import logger, raise_error
@@ -41,61 +42,82 @@ def get_xfm(
     Raises
     ------
     RuntimeError
-        If there is a problem fetching files.
+        If there is a problem cloning the xfm dataset or
+        if there is a problem fetching the xfm file.
 
     """
+    # Set default path for storage
     if xfms_dir is None:
         xfms_dir = Path().home() / "junifer" / "data" / "xfms"
-        logger.debug(f"Creating xfm directory at: {xfms_dir.resolve()}")
-        # Create default junifer data directory if not present
-        xfms_dir.mkdir(exist_ok=True, parents=True)
+
     # Convert str to Path
-    elif not isinstance(xfms_dir, Path):
+    if not isinstance(xfms_dir, Path):
         xfms_dir = Path(xfms_dir)
 
-    # Set local file prefix
-    xfm_file_prefix = f"{src}_to_{dst}"
-    # Set local file dir
-    xfm_file_dir = xfms_dir / xfm_file_prefix
-    # Create local directory if not present
-    xfm_file_dir.mkdir(exist_ok=True, parents=True)
-    # Set file name with extension
-    xfm_file = f"{src}_to_{dst}_Composite.h5"
-    # Set local file path
-    xfm_file_path = xfm_file_dir / xfm_file
-    # Check if the file exists
-    if xfm_file_path.exists():
-        logger.info(
-            f"Found existing xfm file for {src} to {dst} at "
-            f"{xfm_file_path.resolve()}"
+    # Check if the template xfms dataset is installed at storage path
+    is_installed = dl.Dataset(xfms_dir).is_installed()
+    # Use existing dataset
+    if is_installed:
+        logger.debug(
+            f"Found existing template xfms dataset at: {xfms_dir.resolve()}"
         )
-        return xfm_file_path
-
-    # Set URL
-    url = (
-        "https://gin.g-node.org/juaml/human-template-xfms/raw/main/xfms/"
-        f"{xfm_file_prefix}/{xfm_file}"
-    )
-    # Create the file before proceeding
-    xfm_file_path.touch()
-
-    logger.info(f"Downloading xfm file for {src} to {dst} from {url}")
-    # Steam response
-    with httpx.stream("GET", url) as resp:
+        # Set dataset
+        dataset = dl.Dataset(xfms_dir)
+    # Clone a fresh copy
+    else:
+        logger.debug(f"Cloning template xfms dataset to: {xfms_dir.resolve()}")
+        # Clone dataset
         try:
-            resp.raise_for_status()
-        except httpx.HTTPError as exc:
+            dataset = dl.clone(
+                "https://github.com/juaml/human-template-xfms.git",
+                path=xfms_dir,
+                result_renderer="disabled",
+            )
+        except IncompleteResultsError as e:
             raise_error(
-                f"Error response {exc.response.status_code} while "
-                f"requesting {exc.request.url!r}",
+                msg=f"Failed to clone dataset: {e.failed}",
                 klass=RuntimeError,
             )
         else:
-            with open(xfm_file_path, "ab") as f:
-                for chunk in resp.iter_bytes():
-                    f.write(chunk)
+            logger.debug(
+                f"Successfully cloned template xfms dataset to: "
+                f"{xfms_dir.resolve()}"
+            )
 
-    return xfm_file_path
+    # Set file path to retrieve
+    xfm_file_path = (
+        xfms_dir / "xfms" / f"{src}_to_{dst}" / f"{src}_to_{dst}_Composite.h5"
+    )
+
+    # Retrieve file
+    try:
+        got = dataset.get(xfm_file_path, result_renderer="disabled")
+    except IncompleteResultsError as e:
+        raise_error(
+            msg=f"Failed to get file from dataset: {e.failed}",
+            klass=RuntimeError,
+        )
+    else:
+        file_path = Path(got[0]["path"])
+        # Conditional logging based on file fetch
+        status = got[0]["status"]
+        if status == "ok":
+            logger.info(
+                f"Successfully fetched xfm file for {src} to {dst} at "
+                f"{file_path.resolve()}"
+            )
+            return file_path
+        elif status == "notneeded":
+            logger.info(
+                f"Found existing xfm file for {src} to {dst} at "
+                f"{file_path.resolve()}"
+            )
+            return file_path
+        else:
+            raise_error(
+                f"Failed to fetch xfm file for {src} to {dst} at "
+                f"{file_path.resolve()}"
+            )
 
 
 def get_template(

{junifer-0.0.6.dev116 → junifer-0.0.6.dev142}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev116
+Version: 0.0.6.dev142
 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>

{junifer-0.0.6.dev116 → junifer-0.0.6.dev142}/junifer.egg-info/SOURCES.txt

@@ -71,10 +71,12 @@ docs/changes/newsfragments/359.doc
 docs/changes/newsfragments/360.bugfix
 docs/changes/newsfragments/361.misc
 docs/changes/newsfragments/367.enh
+docs/changes/newsfragments/368.enh
 docs/changes/newsfragments/369.bugfix
 docs/changes/newsfragments/370.bugfix
 docs/changes/newsfragments/372.misc
 docs/changes/newsfragments/373.misc
+docs/changes/newsfragments/374.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

junifer-0.0.6.dev116/.github/workflows/docs-preview.yml

@@ -1,68 +0,0 @@
-name: Build and preview docs
-
-on:
-  push:
-    branches-ignore:
-      - 'main'
-    tags-ignore:
-      - v*
-  pull_request:
-    types:
-      - opened
-      - reopened
-      - synchronize
-      - closed
-
-concurrency: preview-${{ github.ref }}
-
-jobs:
-  build-docs:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout source
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        submodules: true
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.x"
-    - name: Check for sudo
-      shell: bash
-      run: |
-        if type sudo >/dev/null 2>&1; then SUDO="sudo"; else SUDO=""; fi
-        echo "SUDO=$SUDO" >> $GITHUB_ENV
-    - name: Install dependencies
-      run: |
-        $SUDO bash -c "$(curl -fsSL http://neuro.debian.net/_files/neurodebian-travis.sh)"
-        $SUDO apt-get update -qq
-        $SUDO apt-get install git-annex-standalone
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -e ".[docs,neurokit2]"
-    - name: Configure git for datalad
-      run: |
-        git config --global user.email "runner@github.com"
-        git config --global user.name "GITHUB CI Runner"
-    - name: Install ANTs
-      run: |
-        echo "++ Add universe repo"
-        sudo add-apt-repository -y universe
-
-        echo "++ Update package manager info"
-        sudo apt-get update -qq
-
-        echo "++ Downloading ANTs"
-        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-2.5.1/bin/* /opt/ants-2.5.1
-        rm ants.zip
-        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
-    - name: Test build docs
-      run: |
-        BUILDDIR=_build/main make -C docs/ local
-    - name: Deploy preview
-      if: github.event_name == 'pull_request'
-      uses: rossjrw/pr-preview-action@v1
-      with:
-        source-dir: docs/_build/main