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Merge pull request #16 from uw-it-aca/pm-update_rstudio_1-4-2
Working R v2021.09.1 Build 372 in 1.4.2 and updated tags
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‎datascience/CHANGELOG.md‎

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# RTTL Jupyter datascience notebook image
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All notable changes to the datascience Jupyter Notebook image will be documented here.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.4.2] - 2021-12-23
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### Changed
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- Increased version for upstream base notebook: jupyter/datascience-notebook:hub-1.4.2
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- Supports JupyterHub v1.4.2
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- Update to JupyterLab v3.2.2
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### Added
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- Added geopandas, folium, and ipyleaflet packages
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## [1.3.0] - 2021-06.14
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### Changed
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- Increased version for upstream base notebook: jupyter/datascience-notebook:hub-1.3.0

‎datascience/Makefile‎

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default: build
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DOCKER_REPO?=gcr.io/uwit-mci-axdd/rttl-datascience-notebook
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DOCKER_TAG?=latest_1-3
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DOCKER_TAG?=latest_1-4-2
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build:
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docker build -t $(DOCKER_REPO):latest -t $(DOCKER_REPO):$(DOCKER_TAG) .
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docker $(DOCKER_REPO):$(DOCKER_TAG) .
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push: build
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docker push $(DOCKER_REPO):$(DOCKER_TAG)
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docker push $(DOCKER_REPO):latest

‎datascience/README.md‎

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- The JupyterLab interface is installed and is set as default
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#### Running Notebook locally
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- `docker run -p 8888:8888 gcr.io/uwit-mci-axdd/rttl-datascience-notebook:latest_1-3`
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- `docker run -p 8888:8888 gcr.io/uwit-mci-axdd/rttl-datascience-notebook:latest_1-4-2`
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- Console output will include localhost url with access token. Add '/lab' to the end of the path portion, eg: `http://127.0.0.1:8888/lab`
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#### Accessing server shell locally
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- `docker run -it --entrypoint /bin/bash gcr.io/uwit-mci-axdd/rttl-datascience-notebook:latest_1-3`
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- `docker run -it --entrypoint /bin/bash gcr.io/uwit-mci-axdd/rttl-datascience-notebook:latest_1-4-2`
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#### Installed packages

‎r/CHANGELOG.md‎

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# RTTL Jupyter R notebook image
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All notable changes to the R Jupyter Notebook image will be documented here.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.4.2] - 2021-12-23
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### Changed
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- Increased version for upstream base notebook: jupyter/r-notebook:hub-1.4.2
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- Supports JupyterHub v1.4.2
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- Update to JupyterLab v3.2.2
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- Update R to v4.1.1
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### Fixed
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- Fixed issue with repr package leading to broken help output
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## [1.3.0] - 2021-06.14
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### Changed
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- Increased version for upstream base notebook: jupyter/r-notebook:hub-1.3.0

‎r/README.md‎

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- The JupyterLab interface is installed and is set as default
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#### Running notebook locally
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- `docker run -p 8888:8888 gcr.io/uwit-mci-axdd/rttl-r-notebook:latest_1-3`
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- `docker run -p 8888:8888 gcr.io/uwit-mci-axdd/rttl-r-notebook:latest_1-4-2`
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- Console output will include localhost url with access token. Add '/lab' to the end of the path portion, eg: `http://127.0.0.1:8888/lab`
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#### Accessing server shell locally
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- `docker run -it --entrypoint /bin/bash gcr.io/uwit-mci-axdd/rttl-r-notebook:latest_1-3`
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- `docker run -it --entrypoint /bin/bash gcr.io/uwit-mci-axdd/rttl-r-notebook:latest_1-4-2`
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#### Installed packages
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via `pip list`

‎rstudio/CHANGELOG.md‎

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# RTTL Jupyter RStudio notebook image
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All notable changes to the RStudio Jupyter Notebook image will be documented here.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.4.2] - 2021-12-23
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### Changed
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- Increased version for upstream base notebook: jupyter/r-notebook:hub-1.4.2
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- Supports JupyterHub v1.4.2
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- Update to JupyterLab v3.2.2
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- Update RStudio Server version 2021.09.1 Build 372
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- Update R to v4.1.1
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### Fixed
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- Fixed issue with repr package leading to broken help output
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- Fixed issue preventing nbgitpuller from working

‎rstudio/Dockerfile‎

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ARG BASE_CONTAINER=jupyter/r-notebook:hub-1.4.2
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FROM $BASE_CONTAINER
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RUN pip install jupyter-rsession-proxy nbgitpuller
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# Base notebook for 1.4.2 uses Ubuntu 20.04 (Focal)
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RUN pip install jupyter-rsession-proxy
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RUN conda install -y -c r r-tidyverse
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# install rstudio-server
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# Note: 1.4x & 1.3x have problems with proxying and auth flow, see: https://github.com/jupyterhub/jupyter-rsession-proxy/issues/97
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USER root
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# WAS: https://download2.rstudio.org/server/trusty/amd64/rstudio-server-1.2.5042-amd64.deb [f6d212f2fdc1e1b4e605256a91b69fed6b61c046374934d262b2c3f1e234c0d6]
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# REMOVED: curl --silent -L --fail http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb > /tmp/libssl.deb && \
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# apt-get install -y /tmp/libssl.deb && \
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# rm /tmp/libssl.deb && \
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# Per: http://cran.rstudio.com/bin/linux/ubuntu/
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RUN apt-get update && \
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apt-get install gdebi-core -y && \
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curl --silent -L --fail https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.0%2B351-amd64.deb > /tmp/rstudio.deb && \
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echo '8ab014f050651d0b3d6d10ff0fcd6ea4873b90581f2ee1d4eaa871280685afae /tmp/rstudio.deb' | shasum -a 256 -c - && \
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curl --silent -L --fail https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.1-372-amd64.deb > /tmp/rstudio.deb && \
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echo 'c58df09468870b89f1796445853dce2dacaa0fc5b7bb1f92b036fa8da1d1f8a3 /tmp/rstudio.deb' | shasum -a 256 -c - && \
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apt-get install -y /tmp/rstudio.deb && \
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rm /tmp/rstudio.deb && \
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apt-get clean
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# These were needed in 1.4x - keeping in case proxy issues are sorted
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# RUN rm /var/lib/rstudio-server/rstudio.sqlite && \
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# chmod -R 777 /var/lib/rstudio-server
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# ENV RSESSION_PROXY_RSTUDIO_1_4=yes
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# Needed in 1.4x
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RUN chmod 777 /var/lib/rstudio-server/rstudio-os.sqlite && \
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chmod -R 777 /usr/sbin/rstudio-server
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ENV RSESSION_PROXY_RSTUDIO_1_4=yes
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ENV PATH=$PATH:/usr/lib/rstudio-server/bin
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USER $NB_USER
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USER $NB_USER
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RUN pip install nbgitpuller && \
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jupyter serverextension enable nbgitpuller --sys-prefix
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# See: https://github.com/uw-it-aca/rttl-notebooks/pull/15
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RUN R -e "devtools::install_github('IRkernel/repr', ref = 'master')"
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RUN R -e "install.packages('IRkernel',repos='http://cran.us.r-project.org')"
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RUN R -e "IRkernel::installspec()"
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ENV RSESSION_PROXY_RSTUDIO_1_4=yes

‎rstudio/Makefile‎

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default: build
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DOCKER_REPO?=gcr.io/uwit-mci-axdd/rttl-rstudio-notebook
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DOCKER_TAG?=fdf878c
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DOCKER_TAG?=latest_1-4-2
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build:
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docker build -t $(DOCKER_REPO):latest -t $(DOCKER_REPO):$(DOCKER_TAG) .
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docker build -t $(DOCKER_REPO):$(DOCKER_TAG) .
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push: build
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docker push $(DOCKER_REPO):latest
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docker push $(DOCKER_REPO):$(DOCKER_TAG)

‎rstudio/README.md‎

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- Installed packages and versions can be viewed in this image's [Dockerfile](Dockerfile) using `pip list` or `conda list`. Output from both command's output is also shown below for convenience.
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#### Running notebook locally
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- `docker run -p 8888:8888 gcr.io/uwit-mci-axdd/rttl-rstudio-notebook:latest`
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- `docker run -p 8888:8888 gcr.io/uwit-mci-axdd/rttl-rstudio-notebook:latest_1-4-2`
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- Console output will include localhost url with access token. Add '/rstudio' to the end of the path portion, eg: `http://127.0.0.1:8888/lab`
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#### Accessing server shell locally
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- `docker run -it --entrypoint /bin/bash gcr.io/uwit-mci-axdd/rttl-rstudio-notebook:latest`
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- `docker run -it --entrypoint /bin/bash gcr.io/uwit-mci-axdd/rttl-rstudio-notebook:latest_1-4-2`
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#### Installed packages
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via `pip list`

‎scipy/CHANGELOG.md‎

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# RTTL Jupyter SciPy notebook image
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All notable changes to the SciPy Jupyter Notebook image will be documented here.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.4.2] - 2021-12-23
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### Changed
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- Increased version for upstream base notebook: jupyter/scipy-notebook:hub-1.4.2
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- Supports JupyterHub v1.4.2
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- Update to JupyterLab v3.2.2
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- Upgrade SciPy version to 1.7.1
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### Added
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- Added astroalign package
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### Fixed
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- Fixed issue with nbclassic by pinning to 0.2.8
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- Fixed issue with biogeme package
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## [1.3.0] - 2021-06.14
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### Changed
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- Increased version for upstream base notebook: jupyter/scipy-notebook:hub-1.3.0

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