Binderize

.github/workflows/binder.yml

@@ -0,0 +1,18 @@
+name: Build Notebook Container
+
+on: [pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout PR
+      uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+
+    - name: test build
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        NO_PUSH: 'true'
+        IMAGE_NAME: "neurohackademy/repo2docker-test"

README.md

@@ -1,4 +1,7 @@
 # Neurohackademy 2020 curriculum
 
 This repository contains the materials for the talks/tutorials in
-NeuroHackademy 2020. Each folder corresponds to one talk/tutorial.
+NeuroHackademy 2020. Each folder corresponds to one talk/tutorial.
+
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/neurohackademy/nh2020-curriculum/master)

binder/.github/workflows/binder.yml

@@ -0,0 +1,18 @@
+name: Build Notebook Container
+
+on: [pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout PR
+      uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+
+    - name: test build
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        NO_PUSH: 'true'
+        IMAGE_NAME: "neurohackademy/repo2docker-test"

binder/apt.txt

@@ -0,0 +1,4 @@
+dnsutils
+iputils-ping
+vim
+nano

binder/environment.yml

@@ -0,0 +1,74 @@
+name: nh
+channels:
+  - conda-forge
+  - plotly
+dependencies:
+  # conda packages for NeuroHackademy
+  - git-annex
+  - graphviz
+  - plotly
+  # -------------------------------------------------------------------------
+
+  # Base packages otherwise pinned in repo2docker, by adding them here we get
+  # more recent versions such as JupyterLab 2.
+  # ref: https://github.com/jupyter/repo2docker/blob/master/repo2docker/buildpacks/conda/environment.yml
+  - python=3.7
+  - ipywidgets
+  - jupyterhub-singleuser
+  - jupyterlab
+  - nbconvert
+  - nbresuse
+  - notebook
+
+  - pip
+  - pip:
+    # pip packages for NeuroHackademy
+    - cython
+    - dask[complete]
+    - datalad
+    - nibabel
+    - indexed-gzip
+    - nilearn
+    - transforms3d
+    - rise
+    - jupytext[myst]
+    - myst-nb
+    - numba
+    - pandas
+    - awscli
+    - s3fs
+    - gcsfs
+    - line_profiler
+    - memory_profiler
+    - graphviz
+    - matplotlib
+    - mne
+    - numpy
+    - scipy
+    - sklearn
+    - neuropythy
+    - ipyvolume==0.6.0a6
+    - pytest
+    - dipy
+    - nitime
+    - xarray
+    - mne
+    - git+https://github.com/arokem/POT.git@pep518
+    - git+https://github.com/arokem/mtw.git@pep518
+    - imageio
+    - ipydatawidgets # dependency for one of plotly's jupyterlab extensions
+    - voila
+    - kaleido # plotly static image export: https://github.com/plotly/plotly.py#static-image-export
+    - nipype
+    - git+https://github.com/nipype/pydra.git@50051730c4bf894ce9ba4833f8c267b5993e0ce0
+    - pydra-ml
+    - git+https://github.com/ReproNim/neurodocker.git@e64f58cc2d93620e6537d9efb0104cc87a99e5ca
+    - pyld
+    - testkraken
+    - seaborn
+    - statsmodels
+    - pytest-notebook  # Testing the notebooks in CI
+    # -----------------------------------------------------------------------
+
+    # Needed by the neurohackademy Helm chart
+    - nbgitpuller

binder/postBuild

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# ipyvolume depend on bqplot as of 27 July 2020
+# plotly instructions: https://github.com/plotly/plotly.py#jupyterlab-support-python-35
+#   - I think jupyterlab-datawidgets is a dependency as well through threejs or
+#     similar. This is a general mess =/
+jupyter labextension install --dev-build=False --minimize=True \
+    @jupyter-voila/jupyterlab-preview \
+    @jupyter-widgets/jupyterlab-manager \
+    bqplot \
+    ipyvolume \
+    jupyterlab-datawidgets \
+    jupyterlab-plotly \
+    plotlywidget \
+ && echo JupyterLab extensions installed.
+
+# Enable use of a /voila path like /lab and /tree
+jupyter serverextension enable --sys-prefix voila
+
+git config --global user.name "Neuro Hacker"
+git config --global user.email [email protected]
+
+mkdir data && \
+ mkdir data/openneuro && \
+ cd data/openneuro && \
+ datalad install ///openfmri/ds000114 && \
+ datalad get ds000114 &&
+ cd ds000114 && \
+ datalad get sub-01/ses-test/func/