MNT: Bump environment (#3132)

Update environment in preparation for release. This includes updates to
ANTs, FSL and h5py, so worth testing separately from the release
process.

Author: effigies

Dockerfile

@@ -103,16 +103,15 @@ RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bi
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
+COPY requirements.txt /tmp/requirements.txt
+WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
 
 ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH"
 RUN /opt/conda/envs/fmriprep/bin/npm install -g svgo@^2.8 [email protected] && \
     rm -r ~/.npm
 
-COPY requirements.txt /tmp/requirements.txt
-RUN /opt/conda/envs/fmriprep/bin/pip install --no-cache-dir -r /tmp/requirements.txt
-
 #
 # Main stage
 #

env.yml

@@ -17,7 +17,7 @@ dependencies:
   - scipy=1.11
   - matplotlib=3.8
   - pandas=2.1
-  - h5py=3.8
+  - h5py=3.10
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.10
   - scikit-image=0.22
@@ -26,12 +26,17 @@ dependencies:
   - graphviz=6.0
   - pandoc=3.1
   # Workflow dependencies: ANTs
-  - ants=2.4.4
-  # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
-  - fsl-bet2=2111.0
-  - fsl-flirt=2111.0
-  - fsl-fast4=2111.0
-  - fsl-fugue=2201.2
+  - ants=2.5.0
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.4)
+  - fsl-bet2=2111.4
+  - fsl-flirt=2111.2
+  - fsl-fast4=2111.3
+  - fsl-fugue=2201.3
   - fsl-mcflirt=2111.0
   - fsl-miscmaths=2203.2
-  - fsl-topup=2203.1
+  - fsl-topup=2203.2
+  - pip
+  - pip:
+    - -r requirements.txt
+variables:
+  FSLOUTPUTTYPE: NIFTI_GZ

requirements.txt

@@ -2,9 +2,9 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile --extra=container
+#    pip-compile --extra=container --strip-extras
 #
-annexremote==1.6.0
+annexremote==1.6.4
     # via
     #   datalad
     #   datalad-next
@@ -35,7 +35,7 @@ cffi==1.16.0
     # via cryptography
 chardet==5.2.0
     # via datalad
-charset-normalizer==3.3.0
+charset-normalizer==3.3.2
     # via requests
 ci-info==0.3.0
     # via
@@ -50,58 +50,57 @@ codecarbon==2.3.1
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-contourpy==1.1.1
+contourpy==1.2.0
     # via matplotlib
-cryptography==41.0.4
+cryptography==41.0.5
     # via secretstorage
 cycler==0.12.1
     # via matplotlib
-cython==3.0.3
-    # via nitime
 datalad==0.19.3
     # via
     #   datalad-next
     #   datalad-osf
     #   fmriprep (pyproject.toml)
-datalad-next==1.0.0
+datalad-next==1.0.2
     # via datalad-osf
 datalad-osf==0.3.0
     # via fmriprep (pyproject.toml)
 distro==1.8.0
     # via datalad
 docopt==0.6.2
     # via num2words
-etelemetry==0.3.0
+etelemetry==0.3.1
     # via nipype
 fasteners==0.19
     # via datalad
-filelock==3.12.4
+filelock==3.13.1
     # via nipype
-fonttools==4.43.1
+fonttools==4.44.0
     # via matplotlib
 formulaic==0.5.2
     # via pybids
 fuzzywuzzy==0.18.0
     # via codecarbon
-greenlet==3.0.0
+greenlet==3.0.1
     # via sqlalchemy
-h5py==3.8.0
+h5py==3.10.0
     # via nitransforms
 humanize==4.8.0
     # via
     #   datalad
     #   datalad-next
 idna==3.4
     # via requests
-imageio==2.31.5
+imageio==2.32.0
     # via scikit-image
 importlib-metadata==6.8.0
     # via keyring
-importlib-resources==6.1.0
+importlib-resources==6.1.1
     # via
     #   niworkflows
     #   sdcflows
-indexed-gzip==1.8.5
+    #   templateflow
+indexed-gzip==1.8.7
     # via smriprep
 interface-meta==1.3.0
     # via formulaic
@@ -126,7 +125,7 @@ joblib==1.3.2
     # via
     #   nilearn
     #   scikit-learn
-keyring==24.2.0
+keyring==24.3.0
     # via datalad
 keyrings-alt==5.0.0
     # via datalad
@@ -149,11 +148,11 @@ lxml==4.9.3
     #   nilearn
     #   prov
     #   svgutils
-mapca==0.0.3
+mapca==0.0.4
     # via tedana
 markupsafe==2.1.3
     # via jinja2
-matplotlib==3.8.0
+matplotlib==3.8.1
     # via
     #   nireports
     #   nitime
@@ -167,10 +166,9 @@ more-itertools==10.1.0
     # via jaraco-classes
 msgpack==1.0.7
     # via datalad
-networkx==3.1
+networkx==3.2.1
     # via
     #   nipype
-    #   nitime
     #   prov
     #   scikit-image
 nibabel==5.1.0
@@ -181,7 +179,6 @@ nibabel==5.1.0
     #   nilearn
     #   nipype
     #   nireports
-    #   nitime
     #   nitransforms
     #   niworkflows
     #   pybids
@@ -206,7 +203,7 @@ nireports==23.1.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-nitime==0.10.1
+nitime==0.10.2
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -222,9 +219,9 @@ niworkflows==1.8.1
     #   fmriprep (pyproject.toml)
     #   sdcflows
     #   smriprep
-num2words==0.5.12
+num2words==0.5.13
     # via pybids
-numpy==1.26.0
+numpy==1.26.2
     # via
     #   bokeh
     #   contourpy
@@ -258,6 +255,7 @@ packaging==23.2
     # via
     #   bokeh
     #   datalad
+    #   etelemetry
     #   fmriprep
     #   fmriprep (pyproject.toml)
     #   matplotlib
@@ -267,7 +265,7 @@ packaging==23.2
     #   niworkflows
     #   scikit-image
     #   smriprep
-pandas==2.1.1
+pandas==2.1.3
     # via
     #   codecarbon
     #   fmriprep
@@ -279,21 +277,21 @@ pandas==2.1.1
     #   pybids
     #   seaborn
     #   tedana
-patool==1.12
+patool==1.15.0
     # via datalad
 pillow==10.0.1
     # via
     #   bokeh
     #   imageio
     #   matplotlib
     #   scikit-image
-platformdirs==3.11.0
+platformdirs==4.0.0
     # via datalad
-prometheus-client==0.17.1
+prometheus-client==0.18.0
     # via codecarbon
 prov==2.0.0
     # via nipype
-psutil==5.9.5
+psutil==5.9.6
     # via
     #   codecarbon
     #   fmriprep
@@ -328,7 +326,7 @@ python-dateutil==2.8.2
     #   nipype
     #   pandas
     #   prov
-python-gitlab==3.15.0
+python-gitlab==4.1.1
     # via datalad
 pytz==2023.3.post1
     # via
@@ -362,7 +360,7 @@ scikit-image==0.22.0
     # via
     #   niworkflows
     #   sdcflows
-scikit-learn==1.3.1
+scikit-learn==1.3.2
     # via
     #   mapca
     #   nilearn
@@ -391,7 +389,7 @@ seaborn==0.13.0
     #   niworkflows
 secretstorage==3.3.3
     # via keyring
-sentry-sdk==1.32.0
+sentry-sdk==1.35.0
     # via fmriprep
 simplejson==3.19.2
     # via nipype
@@ -405,7 +403,7 @@ smriprep==0.12.2
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-sqlalchemy==2.0.21
+sqlalchemy==2.0.23
     # via pybids
 svgutils==0.3.4
     # via
@@ -415,7 +413,7 @@ tedana==23.0.1
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-templateflow==23.0.0
+templateflow==23.1.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -457,15 +455,13 @@ typing-extensions==4.8.0
     #   sqlalchemy
 tzdata==2023.3
     # via pandas
-tzlocal==5.1
+tzlocal==5.2
     # via apscheduler
-urllib3==2.0.6
+urllib3==2.1.0
     # via
     #   requests
     #   sentry-sdk
-wrapt==1.15.0
+wrapt==1.16.0
     # via formulaic
-www-authenticate==0.9.2
-    # via datalad-next
 zipp==3.17.0
     # via importlib-metadata