Jupyter Notebook Upgrade - August 26th, 2020

The All of Us Researcher Workbench’s Jupyter Notebook server was updated on August 26, 2020 to include an upgrade of R from version 3.6 to 4.0 as well as some Python package and R library changes. Note that these updates are only the defaults; you may still choose to modify your runtime by installing new packages or changing package versions from within the notebooks housed in your workspaces. We do not anticipate that this update will have a major impact on standard Python or R notebook code, but it is possible that some existing code may need to be updated to account for the changes. Please contact support@researchallofus.org for help if you experience a notebook breakage and are unable to resolve it. See detailed changes below. 

Timing Upgrade

Jupyter Notebook servers will be upgraded on a rolling basis from August 26th through September 9th  (e.g. while using your notebook during this timeframe, the change may not yet be in effect). If you would like to receive the upgrade to your notebook immediately, you can navigate to the Workspace ‘About’ page, and click the “Reset notebook server” button.

To confirm you received the upgrade, you can check the R version, e.g. from an R notebook, run:

system("R --version", intern=TRUE)

Output:

R version 4.0.2 (2020-06-22) -- "Taking Off Again"

Copyright (C) 2020 The R Foundation for Statistical Computing

Platform: x86_64-pc-linux-gnu (64-bit)

 

Detailed changes:

 python

Packages added:

astunparse

bagit

bgzip

CacheControl

cffi

cli-builder

click

cwltool

Cython

google-crc32c

gs-chunked-io

isodate

lockfile

mypy-extensions

networkx

opt-einsum

prov

psutil

pycparser

python-slugify

QtPy

rdflib

rdflib-jsonld

ruamel.yaml

scandir

schema-salad

shellescape

tensorboard

tensorboard-plugin-wit

tensorflow-estimator

terra-notebook-utils

terra-widgets

text-unidecode

typing-extensions

 

Packages removed:

Click

more-itertools

pluggy

py

pytest

pytest-pylint

whichcraft

 

Packages changed:

arrow: 0.15.5 -> 0.15.8

astroid: 2.3.3 -> 2.4.2

astropy: 4.0 -> 4.0.1.post1

backcall: 0.1.0 -> 0.2.0

bleach: 3.1.1 -> 3.1.5

cachetools: 4.0.0 -> 4.1.1

certifi: 2019.11.28 -> 2020.6.20

confuse: 1.0.0 -> 1.3.0

cookiecutter: 1.7.0 -> 1.7.2

decorator: 4.4.1 -> 4.4.2

google-api-core: 1.16.0 -> 1.22.0

google-auth: 1.11.2 -> 1.20.0

google-cloud-storage: 1.23.0 -> 1.30.0

google-pasta: 0.1.8 -> 0.2.0

google-resumable-media: 0.5.0 -> 0.7.0

googleapis-common-protos: 1.51.0 -> 1.52.0

grpcio: 1.27.2 -> 1.30.0

h5py: 2.7.1 -> 2.10.0

importlib-metadata: 1.5.0 -> 1.7.0

ipykernel: 5.1.4 -> 5.3.4

ipython: 7.12.0 -> 7.17.0

isort: 4.3.21 -> 5.2.2

jedi: 0.16.0 -> 0.17.2

Jinja2: 2.11.1 -> 2.11.2

joblib: 0.11 -> 0.16.0

jupyter-client: 6.0.0 -> 6.1.6

Keras-Preprocessing: 1.1.0 -> 1.1.2

kiwisolver: 1.1.0 -> 1.2.0

llvmlite: 0.31.0 -> 0.33.0

lxml: 4.5.0 -> 4.5.2

Mako: 1.1.1 -> 1.1.3

Markdown: 3.2.1 -> 3.2.2

matplotlib: 3.1.3 -> 3.3.1

nbformat: 5.0.4 -> 5.0.7

numba: 0.48.0 -> 0.50.1

numpy: 1.18.1 -> 1.19.0

packaging: 20.1 -> 20.4

parso: 0.6.1 -> 0.7.1

phik: 0.9.9 -> 0.10.0

Pillow: 7.0.0 -> 7.2.0

pip: 20.0.2 -> 20.2

prometheus-client: 0.7.1 -> 0.8.0

prompt-toolkit: 3.0.3 -> 3.0.5

protobuf: 3.7.1 -> 3.12.4

pydata-google-auth: 0.3.0 -> 1.1.0

Pygments: 2.5.2 -> 2.6.1

pylint: 2.4.4 -> 1.7.2

pyparsing: 2.4.6 -> 2.4.7

pyrsistent: 0.15.7 -> 0.16.0

pysam: 0.15.1 -> 0.15.4

python: 3.7.6 -> 3.7.8

python-apt: 1.6.5+ubuntu0.2 -> 1.6.5+ubuntu0.3

python-datauri: 0.2.8 -> 0.2.9

pytz: 2017.3 -> 2020.1

PyYAML: 5.3 -> 5.3.1

pyzmq: 19.0.0 -> 19.0.2

qtconsole: 4.6.0 -> 4.7.5

requests: 2.23.0 -> 2.24.0

rsa: 4.0 -> 4.6

scikit-learn: 0.20.0 -> 0.21.3

scipy: 1.2.0 -> 1.5.2

setuptools: 45.2.0 -> 49.2.1

tensorflow: 2.0.0a0 -> 2.3.0

urllib3: 1.25.8 -> 1.25.10

wcwidth: 0.1.8 -> 0.2.5

wrapt: 1.11.2 -> 1.12.1

zipp: 3.0.0 -> 3.1.0

 

r

Packages added:

blob

cpp11

isoband

rematch2

 

Packages removed:

clisymbols

fastmap

httpuv

plogr

plyr

reshape2

shiny

sourcetools

xtable

 

Packages changed:

backports: 1.1.5 -> 1.1.8

bigrquery: 1.2.0-1 -> 1.3.1-1

BiocVersion: 3.10.1 -> 3.11.1

bit: 1.1-15.2 -> 4.0.4

bit64: 0.9-7 -> 4.0.2

broom: 0.5.4 -> 0.7.0

callr: 3.4.2 -> 3.4.3

covr: 3.4.0 -> 3.5.0

crosstalk: 1.0.0 -> 1.1.0.1

dbplyr: 1.4.2 -> 1.4.4

devtools: 2.2.2 -> 2.3.1

dplyr: 0.8.4 -> 1.0.1

DT: 0.12 -> 0.14

ellipsis: 0.3.0 -> 0.3.1

forcats: 0.4.0 -> 0.5.0

fs: 1.3.1 -> 1.5.0

gargle: 0.4.0 -> 0.5.0

ggplot2: 3.2.1 -> 3.3.2

git2r: 0.26.1 -> 0.27.1

glue: 1.3.1 -> 1.4.1

googleAuthR: 1.1.1 -> 1.3.0

haven: 2.2.0 -> 2.3.1

htmltools: 0.4.0 -> 0.5.0

httr: 1.4.1 -> 1.4.2

IRkernel: 1.1 -> 1.1.1

jsonlite: 1.6.1 -> 1.7.0

knitr: 1.28 -> 1.29

later: 1.0.0 -> 1.1.0.1

lifecycle: 0.1.0 -> 0.2.0

lubridate: 1.7.4 -> 1.7.9

modelr: 0.1.6 -> 0.1.8

openssl: 1.4.1 -> 1.4.2

pillar: 1.4.3 -> 1.4.6

pkgbuild: 1.0.6 -> 1.1.0

pkgload: 1.0.2 -> 1.1.0

processx: 3.4.2 -> 3.4.3

promises: 1.1.0 -> 1.1.1

ps: 1.3.2 -> 1.3.3

purrr: 0.3.3 -> 0.3.4

r: 3.6.2 -> 4.0.2

rapidjsonr: 1.1 -> 1.2.0

Rcpp: 1.0.3 -> 1.0.5

remotes: 2.1.1 -> 2.2.0

reticulate: 1.14-9001 -> 1.16

rex: 1.1.2 -> 1.2.0

rlang: 0.4.5 -> 0.4.7

rmarkdown: 2.1 -> 2.3

roxygen2: 7.0.2 -> 7.1.1

rversions: 2.0.1 -> 2.0.2

rvest: 0.3.5 -> 0.3.6

scales: 1.1.0 -> 1.1.1

sys: 3.3 -> 3.4

testthat: 2.3.1 -> 2.3.2

tibble: 2.1.3 -> 3.0.3

tidyr: 1.0.2 -> 1.1.1

tidyselect: 1.0.0 -> 1.1.0

tinytex: 0.20 -> 0.25

usethis: 1.5.1 -> 1.6.1

uuid: 0.1-2 -> 0.1-4

vctrs: 0.2.3 -> 0.3.2

withr: 2.1.2 -> 2.2.0

xfun: 0.12 -> 0.16

xml2: 1.2.2 -> 1.3.2

 

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