Merge remote-tracking branch 'upstream/master' into next

Dockerfile

@@ -267,7 +267,7 @@ ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="fMRIPrep" \
       org.label-schema.description="fMRIPrep - robust fMRI preprocessing tool" \
-      org.label-schema.url="http://fmriprep.org" \
+      org.label-schema.url="https://fmriprep.org" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/nipreps/fmriprep" \
       org.label-schema.version=$VERSION \

docs/Makefile

@@ -9,7 +9,7 @@ BUILDDIR      = _build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-	$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http://sphinx-doc.org/)
+	$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from https://www.sphinx-doc.org/)
 endif
 
 # Internal variables.

docs/installation.rst

@@ -94,6 +94,6 @@ Sherlock enables `the following data transfer options
 <https://www.sherlock.stanford.edu/docs/user-guide/storage/data-transfer/>`_.
 
 Alternatively, more comprehensive solutions such as `Datalad
-<http://www.datalad.org/>`_ will handle data transfers with the appropriate
+<https://www.datalad.org/>`_ will handle data transfers with the appropriate
 settings and commands.
 Datalad also performs version control over your data.

docs/links.rst

@@ -1,5 +1,5 @@
-.. _Nipype: http://nipype.readthedocs.io/en/latest/
-.. _BIDS: http://bids.neuroimaging.io
+.. _Nipype: https://nipype.readthedocs.io/en/latest/
+.. _BIDS: https://bids.neuroimaging.io/
 .. _`BIDS Derivatives`: https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html
 .. _`BEP 011`: https://bids-specification.readthedocs.io/en/bep011/05-derivatives/04-structural-derivatives.html
 .. _`BEP 012`: https://bids-specification.readthedocs.io/en/bep012/05-derivatives/05-functional-derivatives.html

docs/outputs.rst

@@ -607,7 +607,7 @@ the following invocation::
 
   .. [Behzadi2007] Behzadi Y, Restom K, Liau J, Liu TT, A component-based noise correction method
      (CompCor) for BOLD and perfusion-based fMRI. NeuroImage. 2007.
-     doi:`10.1016/j.neuroimage.2007.04.042 <http://doi.org/10.1016/j.neuroimage.2007.04.042>`_
+     doi:`10.1016/j.neuroimage.2007.04.042 <https://doi.org/10.1016/j.neuroimage.2007.04.042>`_
 
   .. [Ciric2017] Ciric R, Wolf DH, Power JD, Roalf DR, Baum GL, Ruparel K, Shinohara RT, Elliott MA,
      Eickhoff SB, Davatzikos C., Gur RC, Gur RE, Bassett DS, Satterthwaite TD.
@@ -617,7 +617,7 @@ the following invocation::
 
   .. [Greve2013] Greve DN, Brown GG, Mueller BA, Glover G, Liu TT,
      A Survey of the Sources of Noise in fMRI. Psychometrika. 2013.
-     doi:`10.1007/s11336-013-9344-2 <http://dx.doi.org/10.1007/s11336-013-9344-2>`_
+     doi:`10.1007/s11336-013-9344-2 <https://doi.org/10.1007/s11336-013-9344-2>`_
 
   .. [Friston1996] Friston KJ1, Williams S, Howard R, Frackowiak RS, Turner R,
      Movement‐Related effects in fMRI time‐series. Magnetic Resonance in Medicine. 1996.
@@ -634,7 +634,7 @@ the following invocation::
 
   .. [Muschelli2014] Muschelli J, Nebel MB, Caffo BS, Barber AD, Pekar JJ, Mostofsky SH,
      Reduction of motion-related artifacts in resting state fMRI using aCompCor. NeuroImage. 2014.
-     doi:`10.1016/j.neuroimage.2014.03.028 <http://doi.org/10.1016/j.neuroimage.2014.03.028>`_
+     doi:`10.1016/j.neuroimage.2014.03.028 <https://doi.org/10.1016/j.neuroimage.2014.03.028>`_
 
   .. [Parkes2018] Parkes L, Fulcher B, Yücel M, Fornito A, An evaluation of the efficacy, reliability,
      and sensitivity of motion correction strategies for resting-state functional MRI. NeuroImage. 2018.
@@ -653,7 +653,7 @@ the following invocation::
      doi:`10.1016/j.neuroimage.2011.10.018 <https://doi.org/10.1016/j.neuroimage.2011.10.018>`_
 
   .. [Power2016] Power JD, A simple but useful way to assess fMRI scan qualities. NeuroImage. 2016.
-     doi:`10.1016/j.neuroimage.2016.08.009 <http://doi.org/10.1016/j.neuroimage.2016.08.009>`_
+     doi:`10.1016/j.neuroimage.2016.08.009 <https://doi.org/10.1016/j.neuroimage.2016.08.009>`_
 
   .. [Provins2022] Provins C et al., Quality control and nuisance regression of fMRI, looking out
      where signal should not be found. Proc. Intl. Soc. Mag. Reson. Med. 31, London (UK). 2022

docs/sphinxext/github_link.py

@@ -30,10 +30,10 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     >>> _linkcode_resolve('py', {'module': 'tty',
     ...                          'fullname': 'setraw'},
     ...                   package='tty',
-    ...                   url_fmt='http://hg.python.org/cpython/file/'
+    ...                   url_fmt='https://hg.python.org/cpython/file/'
     ...                           '{revision}/Lib/{package}/{path}#L{lineno}',
     ...                   revision='xxxx')
-    'http://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
+    'https://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
     """
 
     if revision is None:

docs/usage.rst

@@ -18,7 +18,7 @@ The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data
 Structure)` format, and it must include at least one T1w structural image and
 (unless disabled with a flag) a BOLD series.
 We highly recommend that you validate your dataset with the free, online
-`BIDS Validator <http://bids-standard.github.io/bids-validator/>`_.
+`BIDS Validator <https://bids-standard.github.io/bids-validator/>`_.
 
 The exact command to run *fMRIPRep* depends on the Installation_ method.
 The common parts of the command follow the `BIDS-Apps
@@ -188,27 +188,27 @@ Because processing this emerging type of datasets (*densely sampled neuroimaging
 
 Troubleshooting
 ---------------
-Logs and crashfiles are outputted into the
+Logs and crashfiles are output into the
 ``<output dir>/fmriprep/sub-<participant_label>/log`` directory.
 Information on how to customize and understand these files can be found on the
-`nipype debugging <http://nipype.readthedocs.io/en/latest/users/debug.html>`_
+`Debugging Nipype Workflows <http://nipype.readthedocs.io/en/latest/users/debug.html>`_
 page.
 
 **Support and communication**.
-The documentation of this project is found here: http://fmriprep.readthedocs.org/en/latest/.
+The documentation of this project is found here: https://fmriprep.readthedocs.org/en/latest/.
 
 All bugs, concerns and enhancement requests for this software can be submitted here:
 https://github.com/nipreps/fmriprep/issues.
 
 If you have a problem or would like to ask a question about how to use *fMRIPRep*,
-please submit a question to `NeuroStars.org <http://neurostars.org/tags/fmriprep>`_ with an ``fmriprep`` tag.
+please submit a question to `NeuroStars.org <https://neurostars.org/tag/fmriprep>`_ with an ``fmriprep`` tag.
 NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
 
 Previous questions about *fMRIPRep* are available here:
-http://neurostars.org/tags/fmriprep/
+https://neurostars.org/tag/fmriprep/
 
 To participate in the *fMRIPRep* development-related discussions please use the
-following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging
+following mailing list: https://mail.python.org/mailman/listinfo/neuroimaging
 Please add *[fmriprep]* to the subject line when posting on the mailing list.
 
 

docs/workflows.rst

@@ -274,7 +274,7 @@ See also *sMRIPrep*'s
 Refinement of the brain mask
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Typically, the original brain mask calculated with ``antsBrainExtraction.sh``
-will contain some innaccuracies including small amounts of MR signal from
+will contain some inaccuracies including small amounts of MR signal from
 outside the brain.
 Based on the tissue segmentation of FreeSurfer (located in ``mri/aseg.mgz``)
 and only when the :ref:`Surface Processing <workflows_surface>` step has been

wrapper/pyproject.toml

@@ -49,6 +49,12 @@ raw-options = { version_scheme = "nipreps-calver", root = ".." }
 
 [tool.hatch.build.hooks.vcs]
 version-file = "src/fmriprep_docker/_version.py"
+template = """\
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = {version!r}
+__version_tuple__ = version_tuple = {version_tuple!r}
+"""
 
 [tool.distutils.bdist_wheel]
 universal = true