Merge pull request #860 from effigies/mnt/upgrade

MNT: Update environment definition files
nipreps · Mar 8, 2024 · dc783d8 · dc783d8
2 parents 6edfb38 + 9aadcb8
commit dc783d8
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diff --git a/Dockerfile b/Dockerfile
@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2022 The NiPreps Developers
+# Copyright (c) The NiPreps Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,7 +23,7 @@
 # SOFTWARE.
 
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20230308
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
 # Build wheel
@@ -42,7 +42,7 @@ RUN python -m build /src
 # Utilities for downloading packages
 FROM ${BASE_IMAGE} as downloader
 # Bump the date to current to refresh curl/certificates/etc
-RUN echo "2023.12.12"
+RUN echo "2024.03.08"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     binutils \
@@ -61,7 +61,7 @@ RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/frees
 # AFNI
 FROM downloader as afni
 # Bump the date to current to update AFNI
-RUN echo "2023.07.20"
+RUN echo "2024.03.08"
 RUN mkdir -p /opt/afni-latest \
     && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
     | tar -xz -C /opt/afni-latest --strip-components 1 \
@@ -81,9 +81,16 @@ RUN mkdir -p /opt/afni-latest \
 
 # 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 "2024.03.08"
 RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"

diff --git a/env.yml b/env.yml
@@ -4,23 +4,23 @@ channels:
   - conda-forge
 # Update this ~yearly; last updated April 2023
 dependencies:
-  - python=3.10
+  - python=3.11
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
+  - mkl=2023.2
   - mkl-service=2.4
   # 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
   - scikit-image=0.22
-  - scikit-learn=1.3
+  - scikit-learn=1.4
   # Utilities
-  - graphviz=6.0
+  - graphviz=9.0
   # Workflow dependencies: ANTs
-  - ants=2.5.0
+  - ants=2.5
   # Workflow dependencies: FSL (versions pinned in 6.0.7.4)
   - fsl-bet2=2111.4
   - fsl-flirt=2111.2

diff --git a/requirements.txt b/requirements.txt
@@ -1,16 +1,11 @@
-#
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
-#
-#    pip-compile
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -c - -p 3.11 -o requirements.txt
 astor==0.8.1
     # via formulaic
-attrs==23.1.0
-    # via niworkflows (pyproject.toml)
-bids-validator==1.14.0
+attrs==23.2.0
+bids-validator==1.14.1
     # via pybids
-certifi==2023.11.17
+certifi==2024.2.2
     # via requests
 charset-normalizer==3.3.2
     # via requests
@@ -30,28 +25,23 @@ etelemetry==0.3.1
     # via nipype
 filelock==3.13.1
     # via nipype
-fonttools==4.46.0
+fonttools==4.49.0
     # via matplotlib
 formulaic==0.5.2
     # via pybids
-greenlet==3.0.2
+greenlet==3.0.3
     # via sqlalchemy
 h5py==3.10.0
     # via nitransforms
 idna==3.6
     # via requests
-imageio==2.33.1
+imageio==2.34.0
     # via scikit-image
-importlib-resources==6.1.1 ; python_version < "3.11"
-    # via
-    #   niworkflows (pyproject.toml)
-    #   templateflow
 interface-meta==1.3.0
     # via formulaic
 isodate==0.6.1
     # via rdflib
-jinja2==3.1.2
-    # via niworkflows (pyproject.toml)
+jinja2==3.1.3
 joblib==1.3.2
     # via
     #   nilearn
@@ -61,41 +51,33 @@ kiwisolver==1.4.5
 lazy-loader==0.3
     # via scikit-image
 looseversion==1.3.0
-    # via
-    #   nipype
-    #   niworkflows (pyproject.toml)
-lxml==4.9.3
+    # via nipype
+lxml==5.1.0
     # via
     #   nilearn
     #   prov
     #   svgutils
-markupsafe==2.1.3
+markupsafe==2.1.5
     # via jinja2
-matplotlib==3.8.2
-    # via
-    #   niworkflows (pyproject.toml)
-    #   seaborn
+matplotlib==3.8.3
+    # via seaborn
 networkx==3.2.1
     # via
     #   nipype
     #   prov
     #   scikit-image
-nibabel==5.2.0
+nibabel==5.2.1
     # via
     #   nilearn
     #   nipype
     #   nitransforms
-    #   niworkflows (pyproject.toml)
     #   pybids
-nilearn==0.10.2
-    # via niworkflows (pyproject.toml)
+nilearn==0.10.3
 nipype==1.8.6
-    # via niworkflows (pyproject.toml)
 nitransforms==23.0.1
-    # via niworkflows (pyproject.toml)
 num2words==0.5.13
     # via pybids
-numpy==1.26.2
+numpy==1.26.4
     # via
     #   contourpy
     #   formulaic
@@ -106,7 +88,6 @@ numpy==1.26.2
     #   nilearn
     #   nipype
     #   nitransforms
-    #   niworkflows (pyproject.toml)
     #   pandas
     #   pybids
     #   scikit-image
@@ -121,43 +102,38 @@ packaging==23.2
     #   nibabel
     #   nilearn
     #   nipype
-    #   niworkflows (pyproject.toml)
     #   scikit-image
-pandas==2.1.4
+pandas==2.2.1
     # via
     #   formulaic
     #   nilearn
-    #   niworkflows (pyproject.toml)
     #   pybids
     #   seaborn
-pillow==10.1.0
+pillow==10.2.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
 prov==2.0.0
     # via nipype
 pybids==0.16.4
-    # via
-    #   niworkflows (pyproject.toml)
-    #   templateflow
-pydot==1.4.2
+    # via templateflow
+pydot==2.0.0
     # via nipype
-pyparsing==3.1.1
+pyparsing==3.1.2
     # via
     #   matplotlib
     #   pydot
     #   rdflib
-python-dateutil==2.8.2
+python-dateutil==2.9.0.post0
     # via
     #   matplotlib
     #   nipype
     #   pandas
     #   prov
-pytz==2023.3.post1
+pytz==2024.1
     # via pandas
 pyyaml==6.0.1
-    # via niworkflows (pyproject.toml)
 rdflib==7.0.0
     # via
     #   nipype
@@ -168,52 +144,44 @@ requests==2.31.0
     #   nilearn
     #   templateflow
 scikit-image==0.22.0
-    # via niworkflows (pyproject.toml)
-scikit-learn==1.3.2
+scikit-learn==1.4.1.post1
     # via nilearn
 scipy==1.11.4
     # via
     #   formulaic
     #   nilearn
     #   nipype
     #   nitransforms
-    #   niworkflows (pyproject.toml)
     #   pybids
     #   scikit-image
     #   scikit-learn
-seaborn==0.13.0
-    # via niworkflows (pyproject.toml)
+seaborn==0.13.2
 simplejson==3.19.2
     # via nipype
 six==1.16.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.23
+sqlalchemy==2.0.28
     # via pybids
 svgutils==0.3.4
-    # via niworkflows (pyproject.toml)
-templateflow==23.1.0
-    # via niworkflows (pyproject.toml)
-threadpoolctl==3.2.0
+templateflow==24.0.0
+threadpoolctl==3.3.0
     # via scikit-learn
-tifffile==2023.12.9
+tifffile==2024.2.12
     # via scikit-image
-tqdm==4.66.1
+tqdm==4.66.2
     # via templateflow
 traits==6.3.2
-    # via
-    #   nipype
-    #   niworkflows (pyproject.toml)
+    # via nipype
 transforms3d==0.4.1
-    # via niworkflows (pyproject.toml)
-typing-extensions==4.9.0
+typing-extensions==4.10.0
     # via
     #   formulaic
     #   sqlalchemy
-tzdata==2023.3
+tzdata==2024.1
     # via pandas
-urllib3==2.1.0
+urllib3==2.2.1
     # via requests
 wrapt==1.16.0
     # via formulaic