junifer 0.0.6.dev19__tar.gz → 0.0.6.dev33__tar.gz

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/.github/workflows/ci.yml

@@ -93,16 +93,11 @@ jobs:
       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/
-        FSLOUTPUTTYPE="NIFTI_GZ"
-        FSLMULTIFILEQUIT="TRUE"
-        FSLTCLSH="/opt/fsl/bin/fsltclsh"
-        FSLWISH="/opt/fsl/bin/fslwish"
-        FSLLOCKDIR=""
-        FSLMACHINELIST=""
-        FSLREMOTECALL=""
-        FSLGECUDAQ="cuda.q"
-        echo "/opt/fsl" >> $GITHUB_PATH
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/ --skip_registration
+        echo "FSLDIR=/opt/fsl" >> $GITHUB_ENV
+        echo "FSLOUTPUTTYPE=NIFTI_GZ" >> $GITHUB_ENV
+        echo "FSLMULTIFILEQUIT=TRUE" >> $GITHUB_ENV
+        echo "/opt/fsl/bin" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev19
+Version: 0.0.6.dev33
 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>
@@ -66,6 +66,8 @@ Requires-Dist: julearn==0.3.3; 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: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
+Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; extra == "docs"
+Requires-Dist: setuptools-scm>=8; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/docs/Makefile

@@ -19,24 +19,14 @@ clean:
 	rm -rf auto_examples/
 	rm -rf api/generated/
 
-# For local build
-local: news
-	make _build_local; STATUS=$$?; make news_cleanup; exit $$STATUS
-
-news:
-	@echo "Generating whats_new.rst"
-	cd ../ && towncrier build --keep
-
-news_cleanup:
-	@echo "Cleaning up whats_new.rst"
-	git restore --staged whats_new.rst
-	git restore whats_new.rst
+local:
+	make _build_local; STATUS=$$?; exit $$STATUS
 
 _build_local:
 	sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-html: news
-	make _html; STATUS=$$?; make news_cleanup; exit $$STATUS
+html:
+	make _html; STATUS=$$?; exit $$STATUS
 
 _html:
 	$(SPHINXBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)

junifer-0.0.6.dev33/docs/changes/newsfragments/358.doc

@@ -0,0 +1 @@
+Improve Sphinx configuration and extensions by `Synchon Mandal`_

junifer-0.0.6.dev33/docs/changes/newsfragments/360.bugfix

@@ -0,0 +1 @@
+Enable ``spike`` mapping from ``adhoc`` to ``fmriprep`` for :class:`.fMRIPrepConfoundRemover` by `Leonard Sasse`_ and `Synchon Mandal`_

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/docs/conf.py

@@ -6,36 +6,45 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-import sys
+import datetime
+from functools import partial
 from pathlib import Path
 
+from setuptools_scm import get_version
+
 
 # Check if sphinx-multiversion is installed
 use_multiversion = False
 try:
     import sphinx_multiversion  # noqa: F401
+
     use_multiversion = True
 except ImportError:
     pass
 
-curdir = Path(__file__).parent
-sys.path.append((curdir / "sphinxext").as_posix())
+
+# -- Path setup --------------------------------------------------------------
+
+PROJECT_ROOT_DIR = Path(__file__).parents[1].resolve()
+get_scm_version = partial(get_version, root=PROJECT_ROOT_DIR)
 
 # -- Project information -----------------------------------------------------
 
-project = "junifer"
-copyright = "2023, Authors of junifer"
-author = "Fede Raimondo"
+github_url = "https://github.com"
+github_repo_org = "juaml"
+github_repo_name = "junifer"
+github_repo_slug = f"{github_repo_org}/{github_repo_name}"
+github_repo_url = f"{github_url}/{github_repo_slug}"
+
+project = github_repo_name
+author = f"{project} Contributors"
+copyright = f"{datetime.date.today().year}, {author}"
+
+# The version along with dev tag
+release = get_scm_version(
+    version_scheme="guess-next-dev",
+    local_scheme="no-local-version",
+)
 
 # -- General configuration ---------------------------------------------------
 
@@ -43,16 +52,19 @@ author = "Fede Raimondo"
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    # Built-in extensions:
     "sphinx.ext.autodoc",  # include documentation from docstrings
     "sphinx.ext.autosummary",  # generate autodoc summaries
     "sphinx.ext.doctest",  # test snippets in the documentation
+    "sphinx.ext.extlinks",  # markup to shorten external links
     "sphinx.ext.intersphinx",  # link to other projects` documentation
     "sphinx.ext.mathjax",  # math support for HTML outputs in Sphinx
+    # Third-party extensions:
     "sphinx_gallery.gen_gallery",  # HTML gallery of examples
     "numpydoc",  # support for NumPy style docstrings
-    "gh_substitutions",  # custom GitHub substitutions
     "sphinx_copybutton",  # copy button for code blocks
     "sphinxcontrib.mermaid",  # mermaid support
+    "sphinxcontrib.towncrier.ext",  # towncrier fragment support
 ]
 
 if use_multiversion:
@@ -88,11 +100,8 @@ nitpick_ignore_regex = [
 
 # -- Options for HTML output -------------------------------------------------
 
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-#
 html_theme = "furo"
-
+html_title = "junifer documentation"
 html_logo = "./images/junifer_logo.png"
 
 # These paths are either relative to html_static_path
@@ -146,6 +155,12 @@ intersphinx_mapping = {
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
 }
 
+# -- sphinx.ext.extlinks configuration ---------------------------------------
+
+extlinks = {
+    "gh": (f"{github_repo_url}/issues/%s", "#%s"),
+}
+
 # -- numpydoc configuration --------------------------------------------------
 
 numpydoc_show_class_members = False
@@ -197,3 +212,9 @@ smv_rebuild_tags = False
 smv_tag_whitelist = r"^v\d+\.\d+.\d+$"
 smv_branch_whitelist = r"main"
 smv_released_pattern = r"^tags/v.*$"
+
+# -- sphinxcontrib-towncrier configuration -----------------------------------
+
+towncrier_draft_autoversion_mode = "draft"
+towncrier_draft_include_empty = True
+towncrier_draft_working_directory = PROJECT_ROOT_DIR

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/docs/whats_new.rst

@@ -6,6 +6,8 @@
 What's new
 ==========
 
+.. towncrier-draft-entries:: |release|
+
 .. towncrier release notes start
 
 Junifer 0.0.5 (2024-07-22)

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev19'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev19')
+__version__ = version = '0.0.6.dev33'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev33')

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -93,6 +93,9 @@ FMRIPREP_VALID_NAMES = [
     for t_list in x.values()
     for elem in t_list
 ]
+# NOTE: Check with @fraimondo about the spike mapping intent
+# Add spike_name to FMRIPREP_VALID_NAMES
+FMRIPREP_VALID_NAMES.append("framewise_displacement")
 
 
 @register_preprocessor

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev19
+Version: 0.0.6.dev33
 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>
@@ -66,6 +66,8 @@ Requires-Dist: julearn==0.3.3; 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: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
+Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; extra == "docs"
+Requires-Dist: setuptools-scm>=8; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/junifer.egg-info/SOURCES.txt

@@ -61,7 +61,9 @@ docs/changes/newsfragments/335.enh
 docs/changes/newsfragments/354.feature
 docs/changes/newsfragments/356.bugfix
 docs/changes/newsfragments/357.enh
+docs/changes/newsfragments/358.doc
 docs/changes/newsfragments/359.doc
+docs/changes/newsfragments/360.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -72,7 +74,6 @@ docs/extending/masks.rst
 docs/extending/parcellations.rst
 docs/extending/preprocessor.rst
 docs/images/junifer_logo.png
-docs/sphinxext/gh_substitutions.py
 docs/understanding/data.rst
 docs/understanding/datagrabber.rst
 docs/understanding/datareader.rst

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/junifer.egg-info/requires.txt

@@ -40,6 +40,8 @@ julearn==0.3.3
 sphinx-copybutton<0.5.3,>=0.5.1
 towncrier<23.12.0,>=23.10.0
 sphinxcontrib-mermaid<0.10,>=0.8.1
+sphinxcontrib-towncrier==0.4.0a0
+setuptools-scm>=8
 
 [neurokit2]
 neurokit2>=0.1.7

{junifer-0.0.6.dev19 → junifer-0.0.6.dev33}/pyproject.toml

@@ -85,6 +85,8 @@ docs = [
     "sphinx-copybutton>=0.5.1,<0.5.3",
     "towncrier>=23.10.0,<23.12.0",
     "sphinxcontrib-mermaid>=0.8.1,<0.10",
+    "sphinxcontrib-towncrier==0.4.0a0",
+    "setuptools-scm>=8",
 ]
 
 ################

junifer-0.0.6.dev19/docs/sphinxext/gh_substitutions.py

@@ -1,31 +0,0 @@
-"""Provide GitHub substitutions in Sphinx."""
-
-from docutils.nodes import reference
-from docutils.parsers.rst.roles import set_classes
-
-
-# Taken from MNE-Python
-# adapted from
-# https://doughellmann.com/blog/2010/05/09/defining-custom-roles-in-sphinx/
-
-
-def gh_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
-    """Link to a GitHub issue."""
-    try:
-        # issue/PR mode (issues/PR-num will redirect to pull/PR-num)
-        int(text)
-    except ValueError:
-        # direct link mode
-        slug = text
-    else:
-        slug = "issues/" + text
-    text = "#" + text
-    ref = "https://github.com/juaml/junifer/" + slug
-    set_classes(options)
-    node = reference(rawtext, text, refuri=ref, **options)
-    return [node], []
-
-
-def setup(app):
-    app.add_role("gh", gh_role)
-    return