MNT: Update environment pins (#3226)

## Changes proposed in this pull request

Updates pins for:

1) Python (3.11)
2) NodeJS (20)
3) Scipy numeric stack (conda)
4) ANTs (conda)
5) FSL (conda)
6) Python dependencies (pip)

## Documentation that should be reviewed

Third party dependencies.

Author: effigies

Dockerfile

@@ -23,17 +23,17 @@
 # SOFTWARE.
 
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20230308
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
-# fMRIPrep wheel
+# Build wheel
 #
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/fmriprep
-RUN python -m build /src/fmriprep
+COPY . /src
+RUN python -m build /src
 
 #
 # Download stages
@@ -96,9 +96,16 @@ RUN mkdir /opt/convert3d && \
 
 # Micromamba
 FROM downloader as micromamba
+
+# Install a C compiler to build extensions when needed.
+# traits<6.4 wheels are not available for Python 3.11+, but build easily.
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2023.04.05"
+RUN echo "2024.02.06"
 RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
@@ -112,7 +119,7 @@ RUN micromamba create -y -f /tmp/env.yml && \
 # Check if this is still necessary when updating the base image.
 ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH" \
     UV_USE_IO_URING=0
-RUN npm install -g svgo@^3.0.4 bids-validator@^1.13.1 && \
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
     rm -r ~/.npm
 
 #
@@ -249,7 +256,7 @@ RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/e
     && chmod +x /usr/local/bin/msm
 
 # Installing FMRIPREP
-COPY --from=src /src/fmriprep/dist/*.whl .
+COPY --from=src /src/dist/*.whl .
 RUN pip install --no-cache-dir $( ls *.whl )[container,test]
 
 RUN find $HOME -type d -exec chmod go=u {} + && \

docs/installation.rst

@@ -85,12 +85,12 @@ nipype_.
 not handled by the Python's packaging system (Pypi) used to deploy
 the ``fmriprep`` package:
 
-- FSL_ (version 6.0.6.2)
-- ANTs_ (version 2.4.4)
-- AFNI_ (version 23.1.05)
-- `C3D <https://sourceforge.net/projects/c3d/>`_ (version 1.3.0)
+- FSL_ (version 6.0.7.7)
+- ANTs_ (version 2.5.1)
+- AFNI_ (version 24.0.05)
+- `C3D <https://sourceforge.net/projects/c3d/>`_ (version 1.4.0)
 - FreeSurfer_ (version 7.3.2)
-- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.8.0)
+- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.14.0)
 - `connectome-workbench <https://www.humanconnectome.org/software/connectome-workbench>`_ (version 1.5.0)
 
 Not running on a local machine? - Data transfer

env.yml

@@ -2,36 +2,36 @@ name: fmriprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated April 2023
+# Update this ~yearly; last updated Jan 2024
 dependencies:
-  - python=3.10
+  - python=3.11
   # Needed for svgo and bids-validator; consider moving to deno
-  - nodejs=18
+  - nodejs=20
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
-  - mkl-service=2.4
+  - mkl=2023.2.0
+  - mkl-service=2.4.0
   # git-annex for templateflow users with DataLad superdatasets
   - git-annex=*=alldep*
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
   - scipy=1.11
   - matplotlib=3.8
-  - pandas=2.1
+  - pandas=2.2
   - h5py=3.10
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.10
   - scikit-image=0.22
-  - scikit-learn=1.3
+  - scikit-learn=1.4
   # Utilities
-  - graphviz=6.0
+  - graphviz=9.0
   - pandoc=3.1
   # Workflow dependencies: ANTs
-  - ants=2.5.0
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.4)
+  - ants=2.5
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
   - fsl-bet2=2111.4
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3
-  - fsl-fugue=2201.3
+  - fsl-fugue=2201.4
   - fsl-mcflirt=2111.0
   - fsl-miscmaths=2203.2
   - fsl-topup=2203.2