MNT: Update environment (#3073)

We've got a couple dependabot nudges. Running `pip-compile`, but with
the following manual edits:

1) No change to nipreps dependencies. This also means skipping
`importlib_resources`.
2) Avoiding scipy 1.11 for now, as networkx has pinned `!= 1.11.0, !=
1.11.1`.

Assuming this passes, I'm going to see about relaxing the tedana pin.

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=1.24
-  - 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
-  - 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

@@ -32,9 +32,9 @@ dependencies = [
     "psutil >= 5.4",
     "pybids >= 0.15.2",
     "requests",
-    "sdcflows  @ git+https://github.com/nipreps/sdcflows.git@master",
+    "sdcflows  @ git+https://github.com/nipreps/sdcflows.git@maint/2.5.x",
     "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
-    "tedana ~= 0.0.9",
+    "tedana >= 0.0.9",
     "templateflow >= 23.0.0",
     "toml",
     "codecarbon",
@@ -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",