Merge pull request #361 from effigies/mnt/env

MNT: Update installation environment

.circleci/config.yml

@@ -128,6 +128,8 @@ jobs:
                 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                 --build-arg VCS_REF=`git rev-parse --short HEAD` \
                 --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" .
+      - run:
+          command: docker images
       - run:
           name: Check Docker image
           command: |

Dockerfile

@@ -77,13 +77,6 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dAutomask" -or \
         -name "3dvolreg" \) -delete
 
-# ANTs 2.4.4
-FROM downloader as ants
-RUN mkdir -p /opt && \
-    curl -sSLO "https://github.com/ANTsX/ANTs/releases/download/v2.4.4/ants-2.4.4-ubuntu-22.04-X64-gcc.zip" && \
-    unzip ants-2.4.4-ubuntu-22.04-X64-gcc.zip -d /opt && \
-    rm ants-2.4.4-ubuntu-22.04-X64-gcc.zip
-
 # Connectome Workbench 1.5.0
 FROM downloader as workbench
 RUN mkdir /opt/workbench && \
@@ -172,7 +165,6 @@ RUN apt-get update -qq \
 # Install files from stages
 COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
 COPY --from=afni /opt/afni-latest /opt/afni-latest
-COPY --from=ants /opt/ants-2.4.4 /opt/ants
 COPY --from=workbench /opt/workbench /opt/workbench
 
 # Simulate SetUpFreeSurfer.sh
@@ -197,11 +189,6 @@ ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
     AFNI_PLUGINPATH="/opt/afni-latest"
 
-# ANTs config
-ENV ANTSPATH="/opt/ants" \
-    PATH="/opt/ants/bin:$PATH" \
-    LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
-
 # Workbench config
 ENV PATH="/opt/workbench/bin_linux64:$PATH" \
     LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"

env.yml

@@ -11,20 +11,19 @@ dependencies:
   - mkl=2022.1
   - mkl-service=2.4
   # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.24
-  - scipy=1.10
-  - matplotlib=3.7
+  - numpy=1.25
+  - scipy=1.11
+  - matplotlib=3.7,!=3.7.2
   - pandas=2.0
   - h5py=3.8
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.20
-  - scikit-learn=1.2
+  - scikit-image=0.21
+  - scikit-learn=1.3
   # Utilities
   - graphviz=6.0
   - pandoc=3.1
-  # Workflow dependencies: Convert3D
-  - convert3d=1.3.0
-  - libitk=5.2  # 5.3 fails with c3d
+  # 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

requirements.txt

@@ -8,15 +8,15 @@ astor==0.8.1
     # via formulaic
 attrs==23.1.0
     # via niworkflows
-bids-validator==1.11.0
+bids-validator==1.12.0
     # via pybids
-certifi==2023.5.7
+certifi==2023.7.22
     # via requests
-charset-normalizer==3.1.0
+charset-normalizer==3.2.0
     # via requests
 ci-info==0.3.0
     # via etelemetry
-click==8.1.3
+click==8.1.7
     # via
     #   nipype
     #   pybids
@@ -30,42 +30,42 @@ etelemetry==0.3.0
     # via nipype
 filelock==3.12.2
     # via nipype
-fonttools==4.40.0
+fonttools==4.42.1
     # via matplotlib
 formulaic==0.5.2
     # via pybids
 greenlet==2.0.2
     # via sqlalchemy
-h5py==3.8.0
+h5py==3.9.0
     # via nitransforms
 idna==3.4
     # via requests
-imageio==2.31.1
+imageio==2.31.2
     # via scikit-image
-indexed-gzip==1.7.1
+indexed-gzip==1.8.3
     # via smriprep (pyproject.toml)
 interface-meta==1.3.0
     # via formulaic
 isodate==0.6.1
     # via rdflib
 jinja2==3.1.2
     # via niworkflows
-joblib==1.2.0
+joblib==1.3.2
     # via
     #   nilearn
     #   scikit-learn
-kiwisolver==1.4.4
+kiwisolver==1.4.5
     # via matplotlib
-lazy-loader==0.2
+lazy-loader==0.3
     # via scikit-image
 lockfile==0.12.2
     # via smriprep (pyproject.toml)
-looseversion==1.2.0
+looseversion==1.3.0
     # via
     #   nipype
     #   niworkflows
     #   smriprep (pyproject.toml)
-lxml==4.9.2
+lxml==4.9.3
     # via
     #   nilearn
     #   prov
@@ -96,13 +96,13 @@ nipype==1.8.6
     # via
     #   niworkflows
     #   smriprep (pyproject.toml)
-nitransforms==23.0.0
+nitransforms==23.0.1
     # via niworkflows
-niworkflows==1.8.0
+niworkflows==1.8.1
     # via smriprep (pyproject.toml)
 num2words==0.5.12
     # via pybids
-numpy==1.24.3
+numpy==1.25.2
     # via
     #   contourpy
     #   formulaic
@@ -132,28 +132,28 @@ packaging==23.1
     #   niworkflows
     #   scikit-image
     #   smriprep (pyproject.toml)
-pandas==2.0.2
+pandas==2.0.3
     # via
     #   formulaic
     #   nilearn
     #   niworkflows
     #   pybids
     #   seaborn
-pillow==9.5.0
+pillow==10.0.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
 prov==2.0.0
     # via nipype
-pybids==0.16.1
+pybids==0.16.3
     # via
     #   niworkflows
     #   smriprep (pyproject.toml)
     #   templateflow
 pydot==1.4.2
     # via nipype
-pyparsing==3.1.0
+pyparsing==3.0.9
     # via
     #   matplotlib
     #   pydot
@@ -168,11 +168,11 @@ pytz==2023.3
     # via pandas
 pywavelets==1.4.1
     # via scikit-image
-pyyaml==6.0
+pyyaml==6.0.1
     # via
     #   niworkflows
     #   smriprep (pyproject.toml)
-rdflib==6.3.2
+rdflib==7.0.0
     # via
     #   nipype
     #   prov
@@ -181,11 +181,11 @@ requests==2.31.0
     #   etelemetry
     #   nilearn
     #   templateflow
-scikit-image==0.20.0
+scikit-image==0.21.0
     # via niworkflows
-scikit-learn==1.2.2
+scikit-learn==1.3.0
     # via nilearn
-scipy==1.10.1
+scipy==1.11.2
     # via
     #   formulaic
     #   nilearn
@@ -203,33 +203,33 @@ six==1.16.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.16
+sqlalchemy==2.0.20
     # via pybids
 svgutils==0.3.4
     # via niworkflows
 templateflow==23.0.0
     # via
     #   niworkflows
     #   smriprep (pyproject.toml)
-threadpoolctl==3.1.0
+threadpoolctl==3.2.0
     # via scikit-learn
-tifffile==2023.4.12
+tifffile==2023.8.25
     # via scikit-image
-tqdm==4.65.0
+tqdm==4.66.1
     # via templateflow
 traits==6.3.2
     # via
     #   nipype
     #   niworkflows
 transforms3d==0.4.1
     # via niworkflows
-typing-extensions==4.6.3
+typing-extensions==4.7.1
     # via
     #   formulaic
     #   sqlalchemy
 tzdata==2023.3
     # via pandas
-urllib3==2.0.3
+urllib3==2.0.4
     # via requests
 wrapt==1.15.0
     # via formulaic