Release Notes

For: uc-cdis/containers

Notes since tag: 1.1.0

Notes to tag/commit: 1.2.0

Generated: 2023-08-02

New Features

Add Jupyter with Nextflow Dockerfile and image build workflow (#113)
Small updates to notebooks, new base ws image, and update python package
versions (#98)
add Anvil 1000g notebook and IBD notebook (#78)
keeping master branch and feat/brhbuilder branch synced (#77)
Add ACTT1_accessclinical_notebook.ipynb notebook to BRH (#70)
VADC specific Jupyter Notebooks with SQL Server related tools & libraries
(#67)
Automatically build workspace images for notebooks pushed to
HEAL-notebooks/ (#53)
Adding import requirements for a HEAL WS notebook that fell through the
cracks (#59)
Add docker file for jupyter 6.4.0 with additional packages (#58)
Add new Jupyter/R image with latest python and R version. (#57)
Adds a container for a jupyter workspace with Stata functionality (#51)
Stata workspaces have Stata software pre-installed but unlicensed. Users
can bring licenses and leave them in their ~/pd/ directories (#51)
Workbook and custom docker image for HEAL (#47)
jupyter-covid19: Add google_mobility notebook (#45)

Github workflow python print statements updated to use GITBHUB_OUTPUT,
set-output deprecated (#105)
Pin s3-cp-action in stata workflow to suppress path error in aws command.
(#104)
Github workflow updated to use GITBHUB_OUTPUT, set-output deprecated (#101)
Remove duplicate conda install statements from the dockerfile (#98)
fix jupyter lab issue by pinning services (#90)
Fix the errors when using pip cmd. (#68)
Change covid19-notebooks/welcome.html path to use variable instead of hard
coded version number (#43)

Update Gen3-licensed Stata notebook to utilize Gen3 limited licenses.
(#107)
update jupyter-vadc base image to datascience-notebook:2023-04-10 (#93)
Add frictionless library (#87)
Add a python3.9 image with data science libraries (#83)
add scikit-allel installation (#74)
Add tcga_prad analysis notebook (#75)
Reduce base image size from 1.8Gb+ to ~450Mb (+dependencies) (#53)
Some notebooks in
https://github.com/uc-cdis/covid19-tools/tree/master/covid19-notebooks are
not in the PRC workspace. This PR added all missing notebooks and related
files. (#64)
Add gen3 sdk to jupyter-6.4.0-with-base-packages docker file (#63)
Change file title and file name of BACPAC and JCOIN ipynb notebooks (#61)
Updating HEAL Prod tutorial notebooks (#60)
Split the workspace containing the HEAL notebook into separate BACPAC and
JCOIN workspaces (#52)

Notebook image naming is now distinct from user licensed Stata notebook
(#107)
3 ways to reference an image for hatchery config: (#53)
quay.io/cdis/heal-notebooks:{notebook}__latest (#53)
quay.io/cdis/heal-notebooks:{notebook}__{branch} (#53)
quay.io/cdis/heal-notebooks:{notebook}__{commit_sha} (#53)
BACPAC and JCOIN notebook workspace images are hosted under
jupyter-bacpac and jupyter-jcoin on quay (#52)
The stata-heal image on quay is built and pushed via github workflow in
order to leverage github secrets to keep the Stata software privately
hosted in s3 (as opposed to other containers which are built via quay
github hooks) (#51)