MNT: Update tedana pin, test on Python 3.12 (#3141)

With ME-ICA/tedana#998 in a release, we can let
bokeh and its dependencies upgrade to their latest versions and start
running tests on Python 3.12.

Author: effigies

.github/workflows/pre-release.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
         install: ['pip']
         check: ['tests']
         pip-flags: ['PRE_PIP_FLAGS']

.github/workflows/stable.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
         install: ['pip']
         check: ['tests']
         pip-flags: ['']

fmriprep/cli/run.py

@@ -202,7 +202,7 @@ def main():
             _copy_any(dseg_tsv, str(config.execution.fmriprep_dir / "desc-aparcaseg_dseg.tsv"))
         errno = 0
     finally:
-        from pkg_resources import resource_filename as pkgrf
+        from .. import data
 
         # Code Carbon
         if config.execution.track_carbon:
@@ -218,7 +218,7 @@ def main():
             config.execution.participant_label,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
-            config=pkgrf("fmriprep", "data/reports-spec.yml"),
+            config=data.load("reports-spec.yml"),
             packagename="fmriprep",
         )
         write_derivative_description(config.execution.bids_dir, config.execution.fmriprep_dir)

fmriprep/cli/workflow.py

@@ -38,12 +38,11 @@ def build_workflow(config_file, retval):
 
     from niworkflows.utils.bids import collect_participants
     from niworkflows.utils.misc import check_valid_fs_license
-    from pkg_resources import resource_filename as pkgrf
 
     from fmriprep.reports.core import generate_reports
     from fmriprep.utils.bids import check_pipeline_version
 
-    from .. import config
+    from .. import config, data
     from ..utils.misc import check_deps
     from ..workflows.base import init_fmriprep_wf
 
@@ -57,7 +56,7 @@ def build_workflow(config_file, retval):
     retval["workflow"] = None
 
     banner = [f"Running fMRIPrep version {version}"]
-    notice_path = Path(pkgrf("fmriprep", "data/NOTICE"))
+    notice_path = data.load.readable("NOTICE")
     if notice_path.exists():
         banner[0] += "\n"
         banner += [f"License NOTICE {'#' * 50}"]
@@ -91,7 +90,7 @@ def build_workflow(config_file, retval):
             config.execution.participant_label,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
-            config=pkgrf("fmriprep", "data/reports-spec.yml"),
+            config=data.load("reports-spec.yml"),
             packagename="fmriprep",
         )
         return retval
@@ -183,9 +182,9 @@ def build_boilerplate(config_file, workflow):
         from pathlib import Path
         from subprocess import CalledProcessError, TimeoutExpired, check_call
 
-        from pkg_resources import resource_filename as pkgrf
+        from .. import data
 
-        bib_text = Path(pkgrf("fmriprep", "data/boilerplate.bib")).read_text()
+        bib_text = data.load.readable("boilerplate.bib").read_text()
         citation_files["bib"].write_text(
             bib_text.replace("fMRIPrep <version>", f"fMRIPrep {config.environment.version}")
         )

fmriprep/tests/test_config.py

@@ -27,10 +27,9 @@
 
 import pytest
 from niworkflows.utils.spaces import format_reference
-from pkg_resources import resource_filename as pkgrf
 from toml import loads
 
-from .. import config
+from .. import config, data
 
 
 def _reset_config():
@@ -59,8 +58,7 @@ def test_reset_config():
 
 def test_config_spaces():
     """Check that all necessary spaces are recorded in the config."""
-    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
-    settings = loads(filename.read_text())
+    settings = loads(data.load.readable("tests/config.toml").read_text())
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)

fmriprep/workflows/bold/registration.py

@@ -33,12 +33,11 @@
 import os.path as op
 import typing as ty
 
-import pkg_resources as pkgr
 from nipype.interfaces import c3, fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 
-from ... import config
+from ... import config, data
 from ...interfaces import DerivativesDataSink
 
 DEFAULT_MEMORY_MIN_GB = config.DEFAULT_MEMORY_MIN_GB
@@ -588,7 +587,7 @@ def init_fsl_bbr_wf(
     else:
         # Should mostly be hit while building docs
         LOGGER.warning("FSLDIR unset - using packaged BBR schedule")
-        flt_bbr.inputs.schedule = pkgr.resource_filename('fmriprep', 'data/flirtsch/bbr.sch')
+        flt_bbr.inputs.schedule = data.load('flirtsch/bbr.sch')
     # fmt:off
     workflow.connect([
         (inputnode, wm_mask, [('t1w_dseg', 'in_seg')]),

fmriprep/workflows/tests/__init__.py

@@ -27,9 +27,10 @@
 from pathlib import Path
 from tempfile import mkdtemp
 
-from pkg_resources import resource_filename as pkgrf
 from toml import loads
 
+from ... import data
+
 
 @contextmanager
 def mock_config():
@@ -40,8 +41,7 @@ def mock_config():
     if not _old_fs:
         os.environ['FREESURFER_HOME'] = mkdtemp()
 
-    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
-    settings = loads(filename.read_text())
+    settings = loads(data.load.readable('tests/config.toml').read_text())
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
@@ -52,7 +52,7 @@ def mock_config():
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())
-    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005')).absolute()
+    config.execution.bids_dir = data.load('tests/ds000005').absolute()
     config.execution.fmriprep_dir = Path(mkdtemp())
     config.execution.init()
 

pyproject.toml

@@ -14,6 +14,7 @@ classifiers = [
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 license = {file = "LICENSE"}
 requires-python = ">=3.10"
@@ -31,9 +32,9 @@ dependencies = [
     "psutil >= 5.4",
     "pybids >= 0.15.2",
     "requests",
-    "sdcflows  @ git+https://github.com/nipreps/sdcflows.git@master",
+    "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
     "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
-    "tedana >= 0.0.9",
+    "tedana >= 23.0.2",
     "templateflow >= 23.0.0",
     "toml",
     "codecarbon",

requirements.txt

@@ -23,11 +23,11 @@ attrs==23.1.0
     #   sdcflows
 bids-validator==1.13.1
     # via pybids
-bokeh==2.2.3
+bokeh==3.3.1
     # via tedana
 boto==2.49.0
     # via datalad
-certifi==2023.7.22
+certifi==2023.11.17
     # via
     #   requests
     #   sentry-sdk
@@ -51,7 +51,9 @@ codecarbon==2.3.1
     #   fmriprep
     #   fmriprep (pyproject.toml)
 contourpy==1.2.0
-    # via matplotlib
+    # via
+    #   bokeh
+    #   matplotlib
 cryptography==41.0.5
     # via secretstorage
 cycler==0.12.1
@@ -75,7 +77,7 @@ fasteners==0.19
     # via datalad
 filelock==3.13.1
     # via nipype
-fonttools==4.44.0
+fonttools==4.45.0
     # via matplotlib
 formulaic==0.5.2
     # via pybids
@@ -91,7 +93,7 @@ humanize==4.8.0
     #   datalad-next
 idna==3.4
     # via requests
-imageio==2.32.0
+imageio==2.33.0
     # via scikit-image
 importlib-metadata==6.8.0
     # via keyring
@@ -116,11 +118,10 @@ jeepney==0.8.0
     # via
     #   keyring
     #   secretstorage
-jinja2==3.0.1
+jinja2==3.1.2
     # via
     #   bokeh
     #   niworkflows
-    #   tedana
 joblib==1.3.2
     # via
     #   nilearn
@@ -152,16 +153,18 @@ mapca==0.0.4
     # via tedana
 markupsafe==2.1.3
     # via jinja2
-matplotlib==3.8.1
+matplotlib==3.8.2
     # via
     #   nireports
     #   nitime
     #   niworkflows
     #   seaborn
     #   smriprep
     #   tedana
-migas==0.3.0
-    # via fmriprep
+migas==0.4.0
+    # via
+    #   file:///home/chris/projects/nipreps/fmriprep-ng
+    #   fmriprep
 more-itertools==10.1.0
     # via jaraco-classes
 msgpack==1.0.7
@@ -213,7 +216,7 @@ nitransforms==23.0.1
     #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.8.1
+niworkflows==1.9.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -267,6 +270,7 @@ packaging==23.2
     #   smriprep
 pandas==2.1.3
     # via
+    #   bokeh
     #   codecarbon
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -277,17 +281,17 @@ pandas==2.1.3
     #   pybids
     #   seaborn
     #   tedana
-patool==1.15.0
+patool==2.0.0
     # via datalad
-pillow==10.0.1
+pillow==10.1.0
     # via
     #   bokeh
     #   imageio
     #   matplotlib
     #   scikit-image
 platformdirs==4.0.0
     # via datalad
-prometheus-client==0.18.0
+prometheus-client==0.19.0
     # via codecarbon
 prov==2.0.0
     # via nipype
@@ -321,7 +325,6 @@ pyparsing==3.1.1
 python-dateutil==2.8.2
     # via
     #   arrow
-    #   bokeh
     #   matplotlib
     #   nipype
     #   pandas
@@ -365,7 +368,7 @@ scikit-learn==1.3.2
     #   mapca
     #   nilearn
     #   tedana
-scipy==1.11.3
+scipy==1.11.4
     # via
     #   formulaic
     #   mapca
@@ -379,7 +382,7 @@ scipy==1.11.3
     #   scikit-learn
     #   sdcflows
     #   tedana
-sdcflows==2.5.1
+sdcflows==2.6.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -389,8 +392,10 @@ seaborn==0.13.0
     #   niworkflows
 secretstorage==3.3.3
     # via keyring
-sentry-sdk==1.35.0
-    # via fmriprep
+sentry-sdk==1.36.0
+    # via
+    #   file:///home/chris/projects/nipreps/fmriprep-ng
+    #   fmriprep
 simplejson==3.19.2
     # via nipype
 six==1.16.0
@@ -399,7 +404,7 @@ six==1.16.0
     #   isodate
     #   osfclient
     #   python-dateutil
-smriprep==0.12.2
+smriprep==0.13.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -409,7 +414,7 @@ svgutils==0.3.4
     # via
     #   nireports
     #   niworkflows
-tedana==23.0.1
+tedana==23.0.2
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -449,7 +454,6 @@ types-python-dateutil==2.8.19.14
     # via arrow
 typing-extensions==4.8.0
     # via
-    #   bokeh
     #   datalad
     #   formulaic
     #   sqlalchemy
@@ -463,5 +467,7 @@ urllib3==2.1.0
     #   sentry-sdk
 wrapt==1.16.0
     # via formulaic
+xyzservices==2023.10.1
+    # via bokeh
 zipp==3.17.0
     # via importlib-metadata