Merge pull request #2601 from nipreps/docker/deps-cleanup

MAINT: Finalize the work we started with the refactor of the Docker image

.circleci/config.yml

@@ -75,17 +75,17 @@ jobs:
           name: Pull nipreps/miniconda
           command: |
             set +e
-            docker pull localhost:5000/miniconda:1.2.0
+            docker pull localhost:5000/miniconda:py38_1.3.2
             success=$?
             set -e
             if [[ "$success" = "0" ]]; then
                 echo "Pulled from local registry"
-                docker tag localhost:5000/miniconda:1.2.0 nipreps/miniconda:1.2.0
+                docker tag localhost:5000/miniconda:py38_1.3.2 nipreps/miniconda:py38_1.3.2
             else
                 echo "Pulling from Docker Hub"
-                docker pull nipreps/miniconda:1.2.0
-                docker tag nipreps/miniconda:1.2.0 localhost:5000/miniconda:1.2.0
-                docker push localhost:5000/miniconda:1.2.0
+                docker pull nipreps/miniconda:py38_1.3.2
+                docker tag nipreps/miniconda:py38_1.3.2 localhost:5000/miniconda:py38_1.3.2
+                docker push localhost:5000/miniconda:py38_1.3.2
             fi
       - run:
           name: Pull fMRIPrep Docker image

Dockerfile

@@ -261,7 +261,7 @@ RUN curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workb
 ENV PATH="/opt/workbench/bin_linux64:$PATH" \
     LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
 
-COPY --from=nipreps/miniconda:1.2.0 /opt/conda /opt/conda
+COPY --from=nipreps/miniconda:py38_1.3.2 /opt/conda /opt/conda
 
 RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
     echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \

docs/conf.py

@@ -43,7 +43,6 @@
     "sphinx.ext.linkcode",
     "sphinxarg.ext",  # argparse extension
     "nipype.sphinxext.plot_workflow",
-    "nbsphinx",
     "sphinxcontrib.napoleon",
 ]
 

setup.cfg

@@ -22,17 +22,14 @@ url = https://github.com/nipreps/fmriprep
 [options]
 python_requires = >=3.7
 install_requires =
-    indexed_gzip >= 0.8.8
     nibabel >= 3.0
     nipype >= 1.5.1
-    nitime
     nitransforms ~= 21.0.0
-    niworkflows ~= 1.4.1
+    niworkflows @ git+https://github.com/nipreps/niworkflows.git@master
     numpy
     pandas
     psutil >= 5.4
     pybids >= 0.12.1
-    pyyaml
     requests
     sdcflows @ git+https://github.com/nipreps/sdcflows.git@master
     smriprep ~= 0.8.0
@@ -51,7 +48,6 @@ packages = find:
 [options.extras_require]
 datalad = datalad
 doc =
-    nbsphinx
     packaging
     pydot >= 1.2.3
     pydotplus