ENV: Update environment with datalad dependencies

Author: effigies

Dockerfile

@@ -244,7 +244,7 @@ ENV MKL_NUM_THREADS=1 \
 
 # Installing FMRIPREP
 COPY --from=src /src/fmriprep/dist/*.whl .
-RUN pip install --no-cache-dir $( ls *.whl )[telemetry,test]
+RUN pip install --no-cache-dir $( ls *.whl )[container,test]
 
 RUN find $HOME -type d -exec chmod go=u {} + && \
     find $HOME -type f -exec chmod go=u {} + && \

env.yml

@@ -10,16 +10,18 @@ dependencies:
   # Intel Math Kernel Library for numpy
   - mkl=2022.1
   - mkl-service=2.4
+  # git-annex for templateflow users with DataLad superdatasets
+  - git-annex=*=alldep*
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.25
-  - scipy=1.10
+  - scipy=1.11
   - matplotlib=3.7
   - pandas=2.0
   - h5py=3.8
   # Dependencies compiled against numpy, best to stick with conda
-  - nitime=0.9
-  - scikit-image=0.20
-  - scikit-learn=1.2
+  - nitime=0.10
+  - scikit-image=0.21
+  - scikit-learn=1.3
   # Utilities
   - graphviz=6.0
   - pandoc=3.1

pyproject.toml

@@ -64,6 +64,12 @@ dev = [
 ]
 duecredit = ["duecredit"]
 resmon = []
+container = [
+    "fmriprep[telemetry]",
+    # templateflow extras
+    "datalad",
+    "datalad-osf",
+]
 telemetry = [
     "migas >= 0.3.0",
     "sentry-sdk >= 1.3",