Merge branch 'master' into TreatWarningsAsErrors

.circleci/config.yml

@@ -696,7 +696,7 @@ jobs:
 
   deploy_pypi:
     docker:
-      - image: cimg/python:3.8.5
+      - image: cimg/python:3.10
     working_directory: /tmp/src/mriqc
     steps:
       - checkout
@@ -725,7 +725,7 @@ jobs:
 
   deploy_docker:
     machine:
-      image: ubuntu-2004:202104-01
+      image: default
     working_directory: /tmp/src/mriqc
     steps:
       - restore_cache:

.mailmap

@@ -68,6 +68,8 @@ Ross Blair <[email protected]> <[email protected]>
 Teresa Gomez <[email protected]>
 Teresa Gomez <[email protected]> teresamg
 Yibei Chen <[email protected]>
+Victor Férat <[email protected]>
+Victor Férat <[email protected]> vferat
 William Triplett <[email protected]>
 Zvi Baratz <[email protected]>
 Zvi Baratz <[email protected]> ZviBaratz

.maint/CONTRIBUTORS.md

@@ -19,6 +19,7 @@ Before every release, unlisted contributors will be invited again to add their n
 | Durnez | Joke | @jokedurnez | 0000-0001-9030-2202 | Department of Psychology, Stanford University, CA, USA |
 | Erramuzpe | Asier | @erramuzpe | 0000-0002-9402-2184 | Computational Neuroimaging Lab, BioCruces Health Research Institute |
 | Fauber | Bennet | @justbennet | | University of Michigan, Ann Arbor, USA |
+| Férat | Victor | @vferat | 0000-0003-1952-7657 | Department of Basic Neurosciences, Université de Genève, Geneva, Switzerland |
 | Garcia-Dias | Rafael | @garciadias | 0000-0001-9332-1580 | Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK |
 | Ghosh | Satrajit S. | @satra | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA |
 | Gomez | Teresa | @teresamg | | The University of Washington eScience Institute, WA, USA |

.maint/update_authors.py

@@ -120,7 +120,7 @@ def get_git_lines(fname='line-contributors.txt'):
 
     git_line_summary_path = shutil.which('git-line-summary')
     if not git_line_summary_path:
-        git_line_summary_path = "git summary --dedup-by-email".split(" ")
+        git_line_summary_path = 'git summary --dedup-by-email'.split(' ')
     else:
         git_line_summary_path = [git_line_summary_path]
 
@@ -233,7 +233,7 @@ def zenodo(
             creator['affiliation'] = creator['affiliation'][0]
 
     Path(zenodo_file).write_text(
-        '%s\n' % json.dumps(zenodo, indent=2)
+        f'{json.dumps(zenodo, indent=2)}\n'
     )
 
 
@@ -301,20 +301,18 @@ def _aslist(value):
 
     print('Authors (%d):' % len(hits))
     print(
-        '%s.'
-        % '; '.join(
+        '{}.'.format('; '.join(
             [
                 '{} \\ :sup:`{}`\\ '.format(i['name'], idx)
                 for i, idx in zip(hits, aff_indexes)
             ]
-        )
+        ))
     )
 
     print(
-        '\n\nAffiliations:\n%s'
-        % '\n'.join(
+        '\n\nAffiliations:\n{}'.format('\n'.join(
             [f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)]
-        )
+        ))
     )
 
 

.zenodo.json

@@ -92,6 +92,12 @@
       "name": "John A. Lee",
       "type": "Researcher"
     },
+    {
+      "orcid": "0000-0002-9661-1396",
+      "affiliation": "Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA",
+      "name": "Jon Haitz Legarreta Gorro\u00f1o",
+      "type": "Researcher"
+    },
     {
       "orcid": "0000-0003-4141-1343",
       "affiliation": "Johns Hopkins Bloomberg School of Public Health, MD, USA",
@@ -104,6 +110,12 @@
       "name": "Ursula A. Tooley",
       "type": "Researcher"
     },
+    {
+      "orcid": "0000-0003-3456-2493",
+      "affiliation": "Psychological and Brain Sciences Department, Dartmouth College, NH, USA",
+      "name": "Yaroslav O. Halchenko",
+      "type": "Researcher"
+    },
     {
       "orcid": "0000-0003-2882-0900",
       "affiliation": "McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA",
@@ -116,12 +128,6 @@
       "name": "James D. Kent",
       "type": "Researcher"
     },
-    {
-      "orcid": "0000-0003-3456-2493",
-      "affiliation": "Psychological and Brain Sciences Department, Dartmouth College, NH, USA",
-      "name": "Yaroslav O. Halchenko",
-      "type": "Researcher"
-    },
     {
       "affiliation": "University of Michigan, Ann Arbor, USA",
       "name": "Bennet Fauber",
@@ -133,12 +139,6 @@
       "name": "Taylor Salo",
       "type": "Researcher"
     },
-    {
-      "orcid": "0000-0002-9661-1396",
-      "affiliation": "Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA",
-      "name": "Jon Haitz Legarreta Gorro\u00f1o",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Max Planck Institute for Human Development, Berlin, Germany",
       "name": "Michael Krause",

CHANGES.rst

@@ -1,3 +1,20 @@
+25.0.0 (TBD)
+============
+A new 25.x series.
+
+CHANGES
+-------
+  * FIX: Decode bytes to produce a string (#1371)
+  * FIX: Containers report wrong version (#1357)
+  * FIX: Elapsed run time format (#1366)
+  * FIX: Passing ``bytes`` into ``str.join()`` (#1356)
+  * FIX: Optimize interface to minimize memory fingerprint (#1351)
+  * ENH: Remove redundant *DIPY* function (#1369)
+  * DOC: Add a HPC troubleshooting section to the documentation (#1349)
+  * DOC: Provide a range of years ending with current for the copyright statement (#1359)
+  * DOC: Fix missing code block start (#1368)
+  * DOC: Reorganize documentation and redirect to *NiPreps* docs (#1367)
+
 24.0.2 (August 26, 2024)
 ========================
 A patch release with bugfixes and enhancements.

Dockerfile

@@ -32,6 +32,9 @@ FROM python:slim AS src
 RUN apt-get update && \
     DEBIAN_FRONTEND=noninteractive \
     apt-get install -y --no-install-recommends git
+ARG VERSION
+ENV SETUPTOOLS_SCM_PRETEND_VERSION=$VERSION
+
 RUN python -m pip install -U pip build
 COPY . /src
 RUN python -m build /src
@@ -197,11 +200,14 @@ RUN find $HOME -type d -exec chmod go=u {} + && \
 # Best practices
 RUN ldconfig
 
+# Update version
+RUN export VERSION=$(python -m mriqc --version | awk '{print $NF}') \
+    && echo "VERSION=$VERSION" >> /etc/environment
+
 WORKDIR /tmp/
 
 # Run mriqc by default
 ENTRYPOINT ["/opt/conda/bin/mriqc"]
-ARG VERSION
 ARG BUILD_DATE
 ARG VCS_REF
 LABEL org.label-schema.build-date=$BUILD_DATE \

docs/source/usage.rst

@@ -11,7 +11,7 @@ Before moving forward, please make sure to have read and understood
 `introductory documentation <https://www.nipreps.org/apps/framework/>`__).
 
 Containerized execution with *Docker* and *Singularity*/*Apptainer*
--------------------------------------------------------
+-------------------------------------------------------------------
 For containerized execution with *Docker* or *Singularity*/*Apptainer*, please
 follow the documentation on the *NiPreps* site, which contains
 tip and troubleshooting guidelines for both
@@ -24,6 +24,30 @@ also includes specific
 The rest of this documentation page applies to both *bare-metal*
 and containerized execution modes.
 
+*MRIQC* can fetch data in *DataLad* datasets
+--------------------------------------------
+As of version 22.0.3, *MRIQC* bundles *DataLad*, enabling automatic
+data fetching in *DataLad* datasets.
+Employing this feature in containerized environments may lead to
+somewhat obscure errors (see, for example,
+`nipreps/mriqc#1307 <https://github.com/nipreps/mriqc/issues/1307>`__).
+If you intend to use *DataLad* datasets, please read carefully
+*NiPreps*' `help for processing DataLad-managed datasets <https://www.nipreps.org/apps/datalad/>`__.
+
+Alternatively, this feature can be disabled by adding
+``--no-datalad-get`` to the command line.
+This will separate *DataLad* management from *MRIQC*'s operation,
+which can be an effective way of debugging issues and averting
+erroneous conditions.
+
+Troubleshooting
+---------------
+If you encounter problems, please check our
+`NiPreps Guidelines for Singularity or Apptainer <https://www.nipreps.org/apps/singularity/>`__.
+Common tips and guidelines that used to be found within *MRIQC*'s
+or *fMRIPrep*'s documentation sites have been relocated in the
+general *NiPreps* website.
+
 A *BIDS Apps* command line interface
 ------------------------------------
 *MRIQC* follows the *BIDS Apps* standard command line interface::
@@ -86,21 +110,13 @@ in :ref:`The MRIQC Reports <reports>`.
     In the ``group`` level, the :abbr:`IQMs (image quality metrics)` extracted in
     first place are combined in a table and the group reports are generated.
 
-*MRIQC* can fetch data in *DataLad* datasets
---------------------------------------------
-As of version 22.0.3, *MRIQC* bundles *DataLad*, enabling automatic
-data fetching in *DataLad* datasets.
-Employing this feature in containerized environments may lead to
-somewhat obscure errors (see, for example,
-`nipreps/mriqc#1307 <https://github.com/nipreps/mriqc/issues/1307>`__).
-If you intend to use *DataLad* datasets, please read carefully
-*NiPreps*' `help for processing DataLad-managed datasets <https://www.nipreps.org/apps/datalad/>`__.
-
-Alternatively, this feature can be disabled by adding
-``--no-datalad-get`` to the command line.
-This will separate *DataLad* management from *MRIQC*'s operation,
-which can be an effective way of debugging issues and averting
-erroneous conditions.
+Command line interface
+......................
+.. argparse::
+   :ref: mriqc.cli.parser._build_parser
+   :prog: mriqc
+   :nodefault:
+   :nodefaultconst:
 
 Running *MRIQC* on HPC with *Singularity*/*Apptainer*
 -----------------------------------------------------
@@ -131,56 +147,6 @@ on ds030 of OpenfMRI:
   maximum of 10GB. Since we saw a memory consumption of 1-2GB during the
   the 1-task example, a rule of thumb may be that each task takes around
   1GB of memory.
-
-Known issues with HPC
-.....................
-
-#. No internet access
-
-    The container needs to download the templates from the internet.
-    If the container does not have internet access, you can download the
-    templates manually using the ``templateflow`` library:
-
-    .. code-block:: python
-
-      import templateflow.api
-      templateflow.api.TF_S3_ROOT = 'http://templateflow.s3.amazonaws.com'
-      templateflow.api.get('MNI152NLin2009cAsym') # change template if needed
-
-    then provide the templates to the container by mounting the ``templateflow`` home directory and setting the ``TEMPLATEFLOW_HOME`` environment variable:
-
-    .. code-block:: bash
-
-      apptainer run -v /path/to/templateflow:/path/to/templates --env TEMPLATEFLOW_HOME=/path/to/templates ...
-
-#. Socket error:
-
-    When running multiple instances of MRIQC on a HPC, you may encounter the following error:
-
-    .. code-block:: python
-
-      OSError: [Errno 98] Address already in use
-
-    To solve this issue, you can try to isolate the container network from the host network by using the ``--network none`` option.
-
-    .. code-block:: bash
-
-      apptainer run --net --network none ...
-
-    This solution might prevent the container from accessing the internet and downloading templates.
-    In this case, you can download the templates manually and provide access to the downloaded files as explained in the previous section.
-
-    .. code-block:: bash
-
-      apptainer run --net --network none -v /path/to/templateflow:/path/to/templates --env TEMPLATEFLOW_HOME=/path/to/templates ...
-
-Command line interface
-----------------------
-.. argparse::
-   :ref: mriqc.cli.parser._build_parser
-   :prog: mriqc
-   :nodefault:
-   :nodefaultconst:
 
 .. topic:: References
 

mriqc/bin/abide2bids.py

@@ -127,7 +127,7 @@ def fetch(args: (str, str, str, str)) -> (str, str):
         out_dir = op.abspath(out_dir)
 
     pkg_id = [u[9:] for u in url.split('/') if u.startswith('NITRC_IR_')][0]
-    sub_file = op.join(tmpdir, '%s.zip' % pkg_id)
+    sub_file = op.join(tmpdir, f'{pkg_id}.zip')
 
     cmd = [_curl_cmd, '-s', '-u', f'{user}:{password}', '-o', sub_file, url]
     sp.check_call(cmd)

mriqc/bin/fs2gif.py

@@ -114,14 +114,14 @@ def main():
         center = np.average([bbox_min, bbox_max], axis=0)
 
         if opts.hist_eq:
-            ref_file = op.join(tmp_sub, '%s.mgz' % subid)
+            ref_file = op.join(tmp_sub, f'{subid}.mgz')
             img = nb.load(op.join(sub_path, 'mri', 'norm.mgz'))
             data = exposure.equalize_adapthist(img.get_fdata(), clip_limit=0.03)
             nb.MGHImage(data, img.affine, img.header).to_filename(ref_file)
 
         if not opts.zoom:
             # Export tiffs for left hemisphere
-            tcl_file = op.join(tmp_sub, '%s.tcl' % subid)
+            tcl_file = op.join(tmp_sub, f'{subid}.tcl')
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write(
@@ -147,7 +147,7 @@ def main():
             if opts.use_xvfb:
                 cmd = _xvfb_run() + cmd
 
-            print('Running tkmedit: %s' % ' '.join(cmd))
+            print('Running tkmedit: {}'.format(' '.join(cmd)))
             sp.call(cmd, env=environ)
             # Convert to animated gif
             print('Stacking coronal slices')
@@ -165,7 +165,7 @@ def main():
 
         else:
             # Export tiffs for left hemisphere
-            tcl_file = op.join(tmp_sub, 'lh-%s.tcl' % subid)
+            tcl_file = op.join(tmp_sub, f'lh-{subid}.tcl')
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write('SetZoomLevel 2')
@@ -184,13 +184,13 @@ def main():
             if opts.use_xvfb:
                 cmd = _xvfb_run() + cmd
 
-            print('Running tkmedit: %s' % ' '.join(cmd))
+            print('Running tkmedit: {}'.format(' '.join(cmd)))
             sp.call(cmd, env=environ)
             # Convert to animated gif
             print('Stacking coronal slices')
 
             # Export tiffs for right hemisphere
-            tcl_file = op.join(tmp_sub, 'rh-%s.tcl' % subid)
+            tcl_file = op.join(tmp_sub, f'rh-{subid}.tcl')
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write('SetZoomLevel 2')
@@ -209,7 +209,7 @@ def main():
             if opts.use_xvfb:
                 cmd = _xvfb_run() + cmd
 
-            print('Running tkmedit: %s' % ' '.join(cmd))
+            print('Running tkmedit: {}'.format(' '.join(cmd)))
             sp.call(cmd, env=environ)
             # Convert to animated gif
             print('Stacking coronal slices')
@@ -260,7 +260,7 @@ def _xvfb_run(wait=5, server_args='-screen 0, 1600x1200x24', logs=None):
 
 
 def _myerror(msg):
-    print('WARNING: Error deleting temporal files: %s' % msg)
+    print(f'WARNING: Error deleting temporal files: {msg}')
 
 
 if __name__ == '__main__':

mriqc/bin/labeler.py

@@ -54,7 +54,7 @@ def main():
                 finished[j - 1] = finished[j - 1] + 1
                 hold[j - 1, i - 1] = int(file[i][j])
     finished = np.divide(np.round(np.divide(finished, total) * 1000), 10)
-    print(f'Completed: {" ".join(["%g%%" % f for f in finished])}')
+    print(f'Completed: {" ".join([f"{f:g}%" for f in finished])}')
     print(f'Total: {np.round(np.divide(np.sum(finished), 3))}%')
     input('Waiting: [enter]')