diff --git a/deployments/utoronto/image/Dockerfile b/deployments/utoronto/image/Dockerfile index 626172b..188a665 100644 --- a/deployments/utoronto/image/Dockerfile +++ b/deployments/utoronto/image/Dockerfile @@ -163,26 +163,25 @@ RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \ USER ${NB_USER} -COPY environment.yml /tmp/ - -RUN conda env update -p ${CONDA_DIR} -f /tmp/environment.yml - -COPY install-jupyter-extensions.bash /tmp/install-jupyter-extensions.bash -RUN /tmp/install-jupyter-extensions.bash - # Set CRAN mirror to rspm before we install anything COPY Rprofile.site /usr/lib/R/etc/Rprofile.site # RStudio needs its own config COPY rsession.conf /etc/rstudio/rsession.conf -# Install IRKernel -RUN r -e "install.packages('IRkernel', version='1.1.1')" && \ - r -e "IRkernel::installspec(prefix='${CONDA_DIR}')" - # Install R packages, cleanup temp package download location COPY install.R /tmp/install.R RUN /tmp/install.R && \ rm -rf /tmp/downloaded_packages/ /tmp/*.rds +COPY requirements.txt /tmp/ +RUN python3 -m pip install -r /tmp/requirements.txt + +COPY install-jupyter-extensions.bash /tmp/install-jupyter-extensions.bash +RUN /tmp/install-jupyter-extensions.bash + +# Install IRKernel +RUN r -e "install.packages('IRkernel', version='1.1.1')" && \ + r -e "IRkernel::installspec(prefix='${CONDA_DIR}')" + # Disable history. ADD ipython_config.py ${CONDA_PREFIX}/etc/ipython/ diff --git a/deployments/utoronto/image/environment.yml b/deployments/utoronto/image/environment.yml deleted file mode 100644 index 425582d..0000000 --- a/deployments/utoronto/image/environment.yml +++ /dev/null @@ -1,59 +0,0 @@ -channels: - - conda-forge -dependencies: - # for jupyter-desktop-server - - websockify - - # language runtimes - - python=3.8.* - - - numpy - - scipy - - matplotlib - - pandas - - seaborn - - sympy - - networkx - - scikit-learn - - beautifulsoup4 - - statsmodels - - nltk - - spacy - - geopandas - # From https://github.com/utoronto-2i2c/jupyterhub-deploy/issues/29 - - astroquery - - astropy - - galpy - - - pip<20.3 - - - pip: - # Infrastructure things - - jupyterlab==2.* - - voila==0.1.23 - - nbgitpuller==0.9.* - - jupyter-resource-usage==0.5.1 - - nbinteract==0.2.5 - - jupytext==1.6.* - - RISE==5.6.1 - - jupyter_contrib_nbextensions==0.5.1 - - jupyter-desktop-server==0.1.3 - - git-credential-helpers==0.2 - - notebook==6.1.6 - - jupyterhub==1.3.0 - - jupyter-server-proxy==1.5.2 - - jupyter-rsession-proxy==1.2 - - jupyter-shiny-proxy==1.1 - - jupyter-tree-download==1.0.1 - - ipywidgets==7.6.2 - # This is temporary (ref: https://github.com/utoronto-2i2c/jupyterhub-deploy/issues/77) - - jedi==0.17.2 - - - datascience - - geojson - - folium - - geopy - - # nbextensions - - jupyterthemes==0.20.0 - - qgrid==1.3.1 diff --git a/deployments/utoronto/image/install-jupyter-extensions.bash b/deployments/utoronto/image/install-jupyter-extensions.bash index ab98fec..caf63ee 100755 --- a/deployments/utoronto/image/install-jupyter-extensions.bash +++ b/deployments/utoronto/image/install-jupyter-extensions.bash @@ -1,13 +1,6 @@ #!/bin/bash set -euo pipefail -jupyter labextension install --debug \ - @jupyter-widgets/jupyterlab-manager@2 \ - @jupyterlab/server-proxy@2.1.1 \ - jupyterlab-jupytext@1.2.1 \ - jupyter-matplotlib@0.7.4 \ - qgrid2@1.1.3 - # Install jupyter-contrib-nbextensions jupyter contrib nbextension install --sys-prefix diff --git a/deployments/utoronto/image/requirements.txt b/deployments/utoronto/image/requirements.txt new file mode 100644 index 0000000..fc16852 --- /dev/null +++ b/deployments/utoronto/image/requirements.txt @@ -0,0 +1,55 @@ +# for jupyter-desktop-server +websockify + +numpy +scipy +matplotlib +pandas +seaborn +sympy +networkx +scikit-learn +beautifulsoup4 +statsmodels +nltk +spacy +geopandas +# From https://github.com/utoronto-2i2c/jupyterhub-deploy/issues/29 +astroquery +astropy +galpy + +# Infrastructure things +jupyterlab==3.* +voila==0.2.10 +nbgitpuller==0.10.* +jupyter-resource-usage==0.5.1 +RISE==5.6.1 +jupyter_contrib_nbextensions==0.5.1 +jupyter-desktop-server==0.1.3 +git-credential-helpers==0.2 +notebook==6.1.6 +jupyterhub==1.3.0 +jupyter-rsession-proxy==1.2 +jupyter-shiny-proxy==1.1 +jupyter-tree-download==1.0.1 +ipywidgets==7.6.2 +traitlets>=5.0 +nbformat>=5.0 +# This is temporary (ref: https://github.com/utoronto-2i2c/jupyterhub-deploy/issues/77) +jedi==0.17.2 + +datascience +geojson +folium +geopy + +# nbextensions +jupyterthemes==0.20.0 +qgrid==1.3.1 + +# JupyterLab extensions +jupyterlab_widgets==1.0.* +jupyter-server-proxy==3.0.2 +jupytext==1.10.* +ipympl==0.7.0 \ No newline at end of file