enh: update docker and binder

Author: oesteban

docker/.dockerignore renamed to .dockerignore

@@ -0,0 +1,57 @@
+FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
+
+USER root
+
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    ca-certificates \
+                    git && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Run post-link scripts during install, but use global to keep out of source tree
+RUN pixi config set --global run-post-link-scripts insecure
+
+# Install dependencies before the package itself to leverage caching
+RUN mkdir /app
+COPY pixi.lock pixi.toml /app
+WORKDIR /app
+
+RUN pixi install -e default --frozen
+RUN pixi shell-hook -e default --as-is | grep -v PATH > /shell-hook.sh
+
+
+FROM jupyter/base-notebook:x86_64-lab-4.0.7
+
+USER root
+
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    curl \
+                    dvipng \
+                    texlive-fonts-recommended \
+                    texlive-fonts-extra \
+                    texlive-latex-extra \
+                    cm-super && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+COPY --link --from=build /app/.pixi/envs/default /app/.pixi/envs/default
+COPY --link --from=build /shell-hook.sh /shell-hook.sh
+RUN cat /shell-hook.sh >> $HOME/.bashrc
+ENV PATH="/app/.pixi/envs/default/bin:$PATH"
+
+ENV NB_USER=jovyan \
+    NB_GROUP=users \
+    NB_UID=1000 \
+    NB_GID=100 \
+    HOME=/home/jovyan
+
+RUN fix-permissions "/home/${NB_USER}"
+# RUN chmod -R ${NB_USER}.${NB_GROUP} "/home/${NB_USER}"
+
+USER ${NB_USER}
+
+WORKDIR ${HOME}
+
+COPY --chown=${NB_UID}:${NB_GID} . ${HOME}/nipreps-book

Dockerfile

@@ -1,6 +1,7 @@
 #!/bin/bash
+set -euxo pipefail
 
-export ANTSPATH="$HOME/src/ants"
-mkdir -p $ANTSPATH
-curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | tar -xzC $ANTSPATH --strip-components 1
-export PATH="$ANTSPATH:$PATH"
+curl -fsSL https://pixi.sh/install.sh | bash
+export PATH="$HOME/.pixi/bin:$PATH"
+
+pixi install --locked

binder/postBuild

@@ -1,12 +1 @@
-attr
-dipy
-git+https://github.com/nipreps/EddyMotionCorrection.git@main
-jupytext
-matplotlib
-nibabel
-nilearn
-git+https://github.com/poldracklab/nitransforms.git@master
-niworkflows >= 1.4.0rc5
-numpy
-pytest
-requests
+# Python dependencies are managed via Pixi. See binder/postBuild for setup steps.