From 51c304d3c3314d11e92246453591054b6b504825 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 11 Oct 2021 23:36:51 +0200
Subject: [PATCH 1/2] enh: include more dependencies with py38_1.3.2

---
 .circleci/config.yml | 10 +++++-----
 Dockerfile           |  2 +-
 setup.cfg            |  6 +-----
 3 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b414cae95..00ebd7c58 100644
--- a/.circleci/config.yml
+++ b/.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
diff --git a/Dockerfile b/Dockerfile
index e0d8469f6..cd190e8b9 100644
--- a/Dockerfile
+++ b/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 && \
diff --git a/setup.cfg b/setup.cfg
index f7efd7609..1a7e8ae3f 100644
--- a/setup.cfg
+++ b/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

From b7e40ef9daa6a42baa2bbcb319c253f57374ef42 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 15 Oct 2021 17:52:51 +0200
Subject: [PATCH 2/2] fix: nbsphinx being loaded by sphinx without using it

---
 docs/conf.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index 94922aeed..d5b15ecef 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -43,7 +43,6 @@
     "sphinx.ext.linkcode",
     "sphinxarg.ext",  # argparse extension
     "nipype.sphinxext.plot_workflow",
-    "nbsphinx",
     "sphinxcontrib.napoleon",
 ]