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2298 Commity (f2f8bb666eb05b452705d85e42197cafc99a8bae)

Autor SHA1 Wiadomość Data
Madhur Tandon f508bf167e replace mamba & conda with micromamba 2022-01-21 11:20:58 +01:00
Simon Li a37a205c0e
Merge pull request #1108 from aplamada/test_R_conda 
[MRG] add tests for R conda
 2022-01-11 10:39:22 +00:00
Simon Li aa17545a9b
Merge pull request #1111 from yuvipanda/no-ppa 
Say 'apt repository' rather than PPA
 2022-01-10 19:02:01 +00:00
YuviPanda c04fff30cd Say 'apt repository' rather than PPA 
PPA is a specific kind of apt repository, hosted on
launchpad.net. We use https://cran.r-project.org/bin/linux/ubuntu/,
which is just a regular apt repository. The PPA terminology
always confused me, so this just clears that up
 2022-01-10 17:43:09 +05:30
Andrei V. Plamada b2b0f758ff
Merge branch 'jupyterhub:main' into test_R_conda 2022-01-08 18:33:59 +01:00
Simon Li 43525352a7
Merge pull request #1107 from yuvipanda/new-r 
Bump default R version to 4.1
 2022-01-08 14:44:37 +00:00
Simon Li 457f718386
Merge pull request #1104 from yuvipanda/rspm 
Get binary R packages from packagemanager.rstudio.com
 2022-01-08 14:43:48 +00:00
Andrei Plamada 8a817eba97 add tests for R conda 2022-01-07 13:37:43 +01:00
YuviPanda 7fd9a3d25f Move 3.6.1 back to 3.6.1-3bionic 
Was accidentally included along with the 3.6.3-1biocnic
upgrade for 3.6
 2022-01-07 11:23:47 +05:30
YuviPanda 3cb3fbf853 Remove unnecessary print() 2022-01-07 11:18:09 +05:30
YuviPanda 05e504a7ce Cleanup some comments 2022-01-07 11:18:02 +05:30
YuviPanda ceb4f8ac4f Hardcode rspm URL as snapshot for IRKernel 2022-01-07 11:17:46 +05:30
YuviPanda e2aefcfbdd Update test to match new default R version 2022-01-05 22:51:27 +05:30
YuviPanda 54636c6ecf Bump default R version to 4.1 
3.6 is almost 4 years old now.
 2022-01-05 22:32:07 +05:30
YuviPanda dbb5ff7c7d Clarify when mran raises valueerror 2022-01-05 21:35:07 +05:30
YuviPanda 8d194b2d1a Remove unused constants 2022-01-05 18:01:15 +05:30
YuviPanda 7c36566bf2 Fix test for particular version of R 3.6 2022-01-05 01:24:10 +05:30
YuviPanda c398de3d88 Update r 3.6 package version pins 
Based on output of apt-cache madison r-base-core
 2022-01-05 01:00:47 +05:30
YuviPanda 0b76e9ea44 Always install IRKernel as a binary package 
And add another R test for R4.0 + rspm
 2022-01-05 00:12:24 +05:30
YuviPanda 5246a0e7c2 Explicitly install r-base-core 
Otherwise latest version was being installed, giving us
R 4.1 even when we ask for 4.0
 2022-01-04 23:51:15 +05:30
YuviPanda ffbace3b38 Check for MRAN differently 2022-01-04 21:50:36 +05:30
YuviPanda d75c0079ad Test that older r snapshots get MRAN 2022-01-04 19:17:06 +05:30
YuviPanda 3ea55e9205 Fix call to rstudio_base_scripts 2022-01-04 19:01:26 +05:30
YuviPanda 685c8a0544 Satisfy black 2022-01-04 18:34:33 +05:30
YuviPanda fd6314d07d Solidify logic for picking rspm vs mran 
- MRAN doesn't seem to have R 4.1 specific snapshots, so let's
  default to RSPM for anything 4.1+.
- Otherwise, snapshot dates in 2022 will result in using rspm
 2022-01-04 18:30:39 +05:30
Tim Head d688997aee
Merge pull request #1105 from manics/update-jupyterlab 2022-01-03 17:52:36 +01:00
Tim Head 020160baf0
Merge pull request #1106 from manics/freeze.py--help 2021-12-28 11:50:35 +01:00
Simon Li 62c0de2282 Add help message to freeze.py 2021-12-23 14:45:41 +00:00
Simon Li da20e9f421 refreeze! 2021-12-23 13:57:27 +00:00
Simon Li 006b0179bf Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 2021-12-23 13:55:47 +00:00
YuviPanda 054b602b13 Add test for r3.6 2021-12-20 18:24:15 +05:30
YuviPanda bca7d849bd Cleanupg RStudio & Shiny server install 
- Install a different version of RStudio for R < 4.1,
  as latest RStudio doesn't seem to support those. And
  newer RStudio isn't supported on these older R versions.
- Cleanup how Shiny is installed - install it with the same
  apt invocation as rstudio (saves time), and install shiny-proxy
  from PyPI instead or GitHub. The release on PyPI is the same
  as our previous GitHub pin.
- Remove outdated comment about different behavior for R 3.6 - I
  think now we get all our R versions from the same apt repo. Plus,
  the conditional was adding more scripts than just adding extra apt
  package repos
 2021-12-20 18:09:24 +05:30
YuviPanda 5d173a349d Make black happy 2021-12-17 15:56:00 +05:30
YuviPanda 1ed05b59c6 Install devtools, shiny & irkernel from a pin 
We were doing this from an old MRAN snapshot. I moved the pin
a little ahead, so IRKernel can also be installed from CRAN
instead of from GitHub. R <= 4.0 gets the old version, and anything
newer gets a more recent version of devtools. This gives us
fast installs for IRkernel with binary packages.

Also add a R 4.0 and R 4.1 test
 2021-12-17 15:52:27 +05:30
YuviPanda 290b008ac5 Fix some code comment references to MRAN 2021-12-17 15:17:44 +05:30
Yuvi Panda 4aa1d154a1
Merge pull request #1100 from TimoRoth/extra_bargs 
Add command line option to pass extra build args
 2021-12-17 14:52:06 +05:30
YuviPanda 476a25998b Get binary R packages from packagemanager.rstudio.com 
packagemanager.rstudio.com is a CRAN mirror provided
by rstudio, with *binary packages* prebuilt for many Linux
Distributions! https://www.rstudio.com/blog/announcing-public-package-manager/
has more excellent detail. It cuts down install times for R packages
by almost 90% in some cases!

Like MRAN (which we use now), they also provide a daily snapshot
of CRAN at that date
(https://docs.rstudio.com/rspm/news/#rstudio-package-manager-2021090).
The URL for CRAN for a particular date can be fetched via an API
call. We call that API, and if there is no snapshot for that date
(anything before Oct 2017), we fall back on to MRAN. Adds a test
to test this fallback.

One possible issue about changing existing binder repos to use binary
builds rather than source builds is that the binary builds sometimes
require you have an apt package installed, and will fail if it is
not. We had to install the zmq library apt package for example -
source installs compile zmq from source, which is where the speedup
comes from. But unlike python wheels or conda packages, these binary
builds are not self-contained - they are linked to apt packages from
the specific distros. So some repos that worked before might fail now.
We can choose a more recent cut-off date to prevent this from happening.
 2021-12-17 14:50:46 +05:30
Timo Rothenpieler ad1dea14ba Use str.partition() for --label argument parsing 2021-12-16 13:38:56 +01:00
Timo Rothenpieler 9f4827132f Add command line option to pass extra build args 2021-12-16 13:35:58 +01:00
Tim Head 1146d4fbde
Merge pull request #1103 from yuvipanda/quieter-r 2021-12-16 12:14:33 +01:00
Tim Head 540001edd8
Merge pull request #1102 from yuvipanda/more-r 2021-12-16 12:09:23 +01:00
YuviPanda e5e00bd1bf Clarify what version of R we are testing for 2021-12-16 15:39:28 +05:30
YuviPanda 0ba4c6851d Fix R syntax error 2021-12-16 14:25:07 +05:30
Min RK 4d6dd532ab
Merge pull request #1097 from TimoRoth/docker_build 
Set labels when building image from Dockerfile
 2021-12-16 09:29:18 +01:00
YuviPanda 2f1fc81dff Quieter R builds 
We redirect stdout (not stderr) of apt-get update and install
in most other places (check out base.py) to not clutter the
output
 2021-12-16 12:29:27 +05:30
YuviPanda 730e622e3f Support R 4.1 2021-12-16 12:16:52 +05:30
Timo Rothenpieler 86df151414 Add --label command line option 2021-11-24 13:22:33 +01:00
Timo Rothenpieler fa512e76bd Set labels in Dockerfile BuildPack 2021-11-24 13:22:33 +01:00
Timo Rothenpieler cf8f3b9195 Add explicit support for labels build parameter 2021-11-24 13:22:33 +01:00
Min RK 00769c0fb2
Merge pull request #847 from yuvipanda/no-node 
Remove nodesource' nodejs
 2021-11-23 13:58:38 +01:00