MNT: Bump version requirements (#3107)

Baseline upgrades before a round of releases. These should incorporate
updated dependencies from nipreps dev versions, but I do not pin the
master/next branches here.

Author: effigies

env.yml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
 # Update this ~yearly; last updated April 2023
 dependencies:
-  - python >=3.10,<3.11
+  - python=3.10
   # Needed for svgo and bids-validator; consider moving to deno
   - nodejs=16
   # Intel Math Kernel Library for numpy
@@ -13,14 +13,14 @@ dependencies:
   # git-annex for templateflow users with DataLad superdatasets
   - git-annex=*=alldep*
   # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.25
+  - numpy=1.26
   - scipy=1.11
-  - matplotlib=3.7,!=3.7.2
-  - pandas=2.0
+  - matplotlib=3.8
+  - pandas=2.1
   - h5py=3.8
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.10
-  - scikit-image=0.21
+  - scikit-image=0.22
   - scikit-learn=1.3
   # Utilities
   - graphviz=6.0

requirements.txt

@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile --extra=container --resolver=backtracking
+#    pip-compile --extra=container
 #
 annexremote==1.6.0
     # via
@@ -13,15 +13,15 @@ apscheduler==3.10.4
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-arrow==1.2.3
+arrow==1.3.0
     # via codecarbon
 astor==0.8.1
     # via formulaic
 attrs==23.1.0
     # via
     #   niworkflows
     #   sdcflows
-bids-validator==1.12.0
+bids-validator==1.13.1
     # via pybids
 bokeh==2.2.3
     # via tedana
@@ -31,11 +31,11 @@ certifi==2023.7.22
     # via
     #   requests
     #   sentry-sdk
-cffi==1.15.1
+cffi==1.16.0
     # via cryptography
 chardet==5.2.0
     # via datalad
-charset-normalizer==3.2.0
+charset-normalizer==3.3.0
     # via requests
 ci-info==0.3.0
     # via
@@ -50,20 +50,20 @@ codecarbon==2.3.1
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-contourpy==1.1.0
+contourpy==1.1.1
     # via matplotlib
-cryptography==41.0.3
+cryptography==41.0.4
     # via secretstorage
-cycler==0.11.0
+cycler==0.12.1
     # via matplotlib
-cython==3.0.0
+cython==3.0.3
     # via nitime
 datalad==0.19.3
     # via
     #   datalad-next
     #   datalad-osf
     #   fmriprep (pyproject.toml)
-datalad-next==1.0.0b3
+datalad-next==1.0.0
     # via datalad-osf
 datalad-osf==0.3.0
     # via fmriprep (pyproject.toml)
@@ -73,17 +73,17 @@ docopt==0.6.2
     # via num2words
 etelemetry==0.3.0
     # via nipype
-fasteners==0.18
+fasteners==0.19
     # via datalad
-filelock==3.12.2
+filelock==3.12.4
     # via nipype
-fonttools==4.42.1
+fonttools==4.43.1
     # via matplotlib
 formulaic==0.5.2
     # via pybids
 fuzzywuzzy==0.18.0
     # via codecarbon
-greenlet==2.0.2
+greenlet==3.0.0
     # via sqlalchemy
 h5py==3.8.0
     # via nitransforms
@@ -93,15 +93,19 @@ humanize==4.8.0
     #   datalad-next
 idna==3.4
     # via requests
-imageio==2.31.1
+imageio==2.31.5
     # via scikit-image
 importlib-metadata==6.8.0
     # via keyring
-indexed-gzip==1.8.3
+importlib-resources==6.1.0
+    # via
+    #   niworkflows
+    #   sdcflows
+indexed-gzip==1.8.5
     # via smriprep
 interface-meta==1.3.0
     # via formulaic
-iso8601==2.0.0
+iso8601==2.1.0
     # via datalad
 isodate==0.6.1
     # via rdflib
@@ -126,7 +130,7 @@ keyring==24.2.0
     # via datalad
 keyrings-alt==5.0.0
     # via datalad
-kiwisolver==1.4.4
+kiwisolver==1.4.5
     # via matplotlib
 lazy-loader==0.3
     # via scikit-image
@@ -149,7 +153,7 @@ mapca==0.0.3
     # via tedana
 markupsafe==2.1.3
     # via jinja2
-matplotlib==3.7.2
+matplotlib==3.8.0
     # via
     #   nireports
     #   nitime
@@ -161,7 +165,7 @@ migas==0.3.0
     # via fmriprep
 more-itertools==10.1.0
     # via jaraco-classes
-msgpack==1.0.5
+msgpack==1.0.7
     # via datalad
 networkx==3.1
     # via
@@ -184,7 +188,7 @@ nibabel==5.1.0
     #   sdcflows
     #   smriprep
     #   tedana
-nilearn==0.10.1
+nilearn==0.10.2
     # via
     #   mapca
     #   nireports
@@ -220,7 +224,7 @@ niworkflows==1.8.1
     #   smriprep
 num2words==0.5.12
     # via pybids
-numpy==1.25.2
+numpy==1.26.0
     # via
     #   bokeh
     #   contourpy
@@ -240,7 +244,6 @@ numpy==1.25.2
     #   niworkflows
     #   pandas
     #   pybids
-    #   pywavelets
     #   scikit-image
     #   scikit-learn
     #   scipy
@@ -251,7 +254,7 @@ numpy==1.25.2
     #   tifffile
 osfclient==0.0.5
     # via datalad-osf
-packaging==23.1
+packaging==23.2
     # via
     #   bokeh
     #   datalad
@@ -264,7 +267,7 @@ packaging==23.1
     #   niworkflows
     #   scikit-image
     #   smriprep
-pandas==2.0.3
+pandas==2.1.1
     # via
     #   codecarbon
     #   fmriprep
@@ -278,13 +281,13 @@ pandas==2.0.3
     #   tedana
 patool==1.12
     # via datalad
-pillow==10.0.0
+pillow==10.0.1
     # via
     #   bokeh
     #   imageio
     #   matplotlib
     #   scikit-image
-platformdirs==3.10.0
+platformdirs==3.11.0
     # via datalad
 prometheus-client==0.17.1
     # via codecarbon
@@ -312,7 +315,7 @@ pydot==1.4.2
     # via nipype
 pynvml==11.5.0
     # via codecarbon
-pyparsing==3.0.9
+pyparsing==3.1.1
     # via
     #   matplotlib
     #   pydot
@@ -327,12 +330,10 @@ python-dateutil==2.8.2
     #   prov
 python-gitlab==3.15.0
     # via datalad
-pytz==2023.3
+pytz==2023.3.post1
     # via
     #   apscheduler
     #   pandas
-pywavelets==1.4.1
-    # via scikit-image
 pyyaml==6.0.1
     # via
     #   bokeh
@@ -357,16 +358,16 @@ requests==2.31.0
     #   templateflow
 requests-toolbelt==1.0.0
     # via python-gitlab
-scikit-image==0.21.0
+scikit-image==0.22.0
     # via
     #   niworkflows
     #   sdcflows
-scikit-learn==1.3.0
+scikit-learn==1.3.1
     # via
     #   mapca
     #   nilearn
     #   tedana
-scipy==1.11.2
+scipy==1.11.3
     # via
     #   formulaic
     #   mapca
@@ -384,15 +385,15 @@ sdcflows==2.5.1
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-seaborn==0.12.2
+seaborn==0.13.0
     # via
     #   nireports
     #   niworkflows
 secretstorage==3.3.3
     # via keyring
-sentry-sdk==1.29.2
+sentry-sdk==1.32.0
     # via fmriprep
-simplejson==3.19.1
+simplejson==3.19.2
     # via nipype
 six==1.16.0
     # via
@@ -404,7 +405,7 @@ smriprep==0.12.2
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-sqlalchemy==2.0.20
+sqlalchemy==2.0.21
     # via pybids
 svgutils==0.3.4
     # via
@@ -426,7 +427,7 @@ threadpoolctl==3.2.0
     # via
     #   scikit-learn
     #   tedana
-tifffile==2023.8.12
+tifffile==2023.9.26
     # via scikit-image
 toml==0.10.2
     # via
@@ -446,23 +447,25 @@ traits==6.3.2
     #   sdcflows
 transforms3d==0.4.1
     # via niworkflows
-typing-extensions==4.7.1
+types-python-dateutil==2.8.19.14
+    # via arrow
+typing-extensions==4.8.0
     # via
     #   bokeh
     #   datalad
     #   formulaic
     #   sqlalchemy
 tzdata==2023.3
     # via pandas
-tzlocal==5.0.1
+tzlocal==5.1
     # via apscheduler
-urllib3==2.0.4
+urllib3==2.0.6
     # via
     #   requests
     #   sentry-sdk
 wrapt==1.15.0
     # via formulaic
 www-authenticate==0.9.2
     # via datalad-next
-zipp==3.16.2
+zipp==3.17.0
     # via importlib-metadata