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1161 Commity (15a1fb6e2d22c013523835280e19c186e605b05f)

Autor SHA1 Wiadomość Data
YuviPanda d72ac15037 Set CRAN mirror URL for R 2022-06-22 08:49:28 -07:00
YuviPanda c123d7bf32 Use new path for Renviron 2022-06-22 08:49:28 -07:00
YuviPanda 4ccbdddeb5 Install package with gdebi 
It fetches dependencies and installs them too, unlike dpkg
 2022-06-22 08:49:28 -07:00
YuviPanda 13250c73d1 Always provide full semver for R version 
Other wise our semver package cries
 2022-06-22 08:49:28 -07:00
YuviPanda 22167c35f0 Actually install the downloaded deb 2022-06-22 08:49:28 -07:00
YuviPanda 965cb15b99 Get R from RStudio managed apt packages 
Might be simpler than getting it from R project managed
apt packages
 2022-06-22 08:49:27 -07:00
Yuvi Panda 0f0fca19a0
Merge pull request #1148 from aplamada/upgrade_rstudio_server_to_2022_02_1 
[MRG] upgrade RStudio Server to v2022.02.1
 2022-06-22 08:36:30 -07:00
Min RK e7524a7b4b
Merge pull request #1156 from CLIP-HPC/fix_server_log 
Fix Read-Only filesystem permission issue for log file
 2022-06-08 11:15:55 +02:00
Dara Adib 991c249141 Remove unused sys import 2022-06-02 20:54:43 -04:00
Dara Adib 49d47b855e Shallow clone HEAD 
Previously repo2docker only performed shallow clones when refspec
was not provided. We now also perform shallow clones if refspec is
explicitly set to HEAD. Binder always specifies a refspec, often
HEAD, so this should improve some build times.
 2022-06-02 20:54:43 -04:00
Ümit Seren 3ee04e34a3 Fix Read-Only filesystem permission issue for log file 2022-05-03 16:05:55 +02:00
Min RK 5df775aac6
keep server log name 2022-04-28 13:07:11 +02:00
Gerald Manipon c09d66fea6 better comment 2022-04-24 17:19:24 -07:00
Gerald Manipon e75c664edb fix join() call 2022-04-19 07:57:58 -07:00
Gerald Manipon 304b1430a5 fix insert call 2022-04-19 05:46:20 -07:00
Gerald Manipon 051c9d36a3 iterate through different log locations 2022-04-18 17:24:49 -07:00
Gerald Manipon 723e5b6907 handle permission issue 2022-04-15 13:26:04 -07:00
YuviPanda 76aacbf3ab Update py3.6 environment one last time 
Updated with previous contents of environment.yml file.
From now on, 3.6 will only get security updates
 2022-04-11 12:31:56 -07:00
YuviPanda 5444850bc4 Update base notebook packages 
- We should stop auto updating 3.6 now, so we can move on to
  newer notebook packages - a new notebook version ought to fix
  issues like https://github.com/2i2c-org/infrastructure/issues/1170
  for example.
- No longer explicitly pin nbconvert, as whatever version notebook
  brings in should be sufficient.
- Bump up ipywidgets and jupyterlab while we're at it.
- No longer pin jupyterhub-singleuser either, as that too works
  properly with 3.7
 2022-04-11 12:31:56 -07:00
Andrei Plamada 190f4cfba8 upgrade RStudio Server to v2022.02.1 2022-03-28 10:01:55 +02:00
Min RK 5cfd798008 handle r version unspecified in environment.yml 2022-02-25 12:03:40 +01:00
yoogottamk c8d86b9b3d
Pass build_args to `render()` during `--no-build` for consistency with regular builds 2022-02-13 12:50:08 +05:30
Min RK 42f83f0af4 use mamba for installs once available 
MAMBA_EXE is mamba itself, not micromamba
use variable everywhere, so switching fully to micromamba can happen in once place,
assuming they are fully compatible (they _almost_ are, except for `env update` vs `install` in a couple places)
 2022-01-28 21:17:09 +01:00
Min RK 84220028bd put micromamba in /usr/local/bin 
instead of tmp, since we want it to stick around.
 2022-01-28 15:58:36 +01:00
Simon Li 8c21b96401
Merge pull request #1123 from yuvipanda/commandline-args 
Allow passing in traitlets via commandline
 2022-01-27 16:50:47 +00:00
Min RK b8a2c88501
Merge pull request #1124 from yuvipanda/extra-args 
Allow passing in extra args to Docker initialization
 2022-01-27 15:49:06 +01:00
Min RK 710d533f75 add `--help-all` support 
a bit funky, since we are combining two separate parsers
 2022-01-27 14:01:45 +01:00
Min RK 7f89926e51
Merge pull request #1062 from wolfv/micromamba 
bootstrap base env with micromamba
 2022-01-27 09:42:53 +01:00
Sylvain Corlay 25bc273a17 Remove -f command-line argument 2022-01-27 01:02:12 +01:00
Simon Li a856862ead Update ipywidgets jupyter-offlinenotebook jupyterlab 
- ipywidgets==7.6.5
- jupyter-offlinenotebook==0.2.2
- jupyterlab==3.2.8
 2022-01-26 18:40:59 +00:00
Yuvi Panda a5df995532
Clarify how kwargs is set 
Co-authored-by: Min RK <benjaminrk@gmail.com>
 2022-01-26 21:32:24 +05:30
Min RK d728a64dd9 get version comparison from semver 
since Python is removing version string parsing from the standard library

moves Julia-specific semver utilities to top-level
 2022-01-26 15:52:09 +01:00
YuviPanda 3af38557ad Allow passing in extra args to Docker initialization 
Puts it in the ContainerEngine interface specific to Docker,
so PodMan can implement its own when necessary.

Fixes https://github.com/jupyterhub/repo2docker/issues/711
 2022-01-26 16:16:46 +05:30
YuviPanda 885cb464b6 Allow passing in traitlets via commandline 
Without this, you *always* needed a repo2docker_config.py
file to configure anything. This PR makes r2d match the
behavior of most traitlets based applications (like jupyter_server,
jupyterhub, nbconvert, etc)

Fixes https://github.com/jupyterhub/repo2docker/issues/1112
 2022-01-26 14:48:11 +05:30
Min RK e3d0a9ae8e
Merge pull request #1119 from yuvipanda/delete-tmp 
Delete /tmp/downloaded_packages after running install.R
 2022-01-26 09:02:27 +01:00
Sylvain Corlay a0f83c012d Re-add call to clean 2022-01-25 23:58:54 +01:00
YuviPanda 6ab41efd4d Delete /tmp/downloaded_packages after running install.R 
This can often leave ~100-200MB in /tmp that isn't re-used
after the image is set up.
 2022-01-25 21:26:16 +05:30
Min RK 945c45299f set USER root after each directive block 
matches expectations in the directive sequences

not strictly required after preassemble because we have no root steps between preassemble and assemble,
so we could remove the `last_user = "root"` there instead

includes regression test
 2022-01-25 14:48:37 +01:00
Min RK ad0034cb2f note why --no-install-recommends is important for r packages 2022-01-25 13:29:15 +01:00
Min RK 19acf46392 remove r-recommended package 
r-recommended is a collection of common CRAN packages,
which cause conflicts when trying to install older R.

These same packages can be regular dependencies retrieved from CRAN.
 2022-01-25 11:38:35 +01:00
Sylvain Corlay 65a36cc3f7 PR review comments: update micromamba, use MAMBA_EXE environment variable 2022-01-21 13:16:33 +01:00
Sylvain Corlay 374efff3dc Fix CI by calling shell init 2022-01-21 11:21:00 +01:00
Sylvain Corlay 5f82b2c8b0 Update micromamba installation 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 7d4ac3b960 Use micromamba 0.17 and install conda & mamba into base env 2022-01-21 11:21:00 +01:00
Wolf Vollprecht e12ffc4a99 use mamba with fixed zstd linkage 2022-01-21 11:21:00 +01:00
Wolf Vollprecht b6091c9265 use wget better 2022-01-21 11:21:00 +01:00
Wolf Vollprecht c96a230962 try nightly 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 245fc1b939 use 0.16.0 2022-01-21 11:21:00 +01:00
Sylvain Corlay 089f6a87a5 Use micromamba 0.15.2 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 3c2ded30be fix rm targets 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 7c4f2a5b4f fix up urls 2022-01-21 11:21:00 +01:00
Madhur Tandon 22d4781809 use strict channel priority 2022-01-21 11:21:00 +01:00
Madhur Tandon 2d27bb2af6 revert back to using install 2022-01-21 11:21:00 +01:00
Madhur Tandon d2a2c070e7 use experimental build of micromamba 2022-01-21 11:21:00 +01:00
Madhur Tandon b08c7dc3b6 use env update instead of install 2022-01-21 11:21:00 +01:00
Madhur Tandon e12c436af2 add MAMBA_EXE environment variable 2022-01-21 11:21:00 +01:00
Madhur Tandon 8926cdc968 minor fixes 2022-01-21 11:21:00 +01:00
Madhur Tandon 9c109f95b4 use latest micromamba and fix MAMBA_ROOT_PREFIX 2022-01-21 11:21:00 +01:00
Madhur Tandon 2e702f0248 rename file and add conda-forge channel to .condarc 2022-01-21 11:21:00 +01:00
Madhur Tandon 3288bca6a4 fix tests + change name of script 2022-01-21 11:21:00 +01:00
Madhur Tandon 6cc7567f2e use micromamba 0.12.2 2022-01-21 11:21:00 +01:00
Madhur Tandon f9388c3200 use latest micromamba 2022-01-21 11:21:00 +01:00
Madhur Tandon f508bf167e replace mamba & conda with micromamba 2022-01-21 11:20:58 +01:00
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
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
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 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 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 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 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
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 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
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 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 7aee21fd05 add nodejs to locked py35 env 
updates a bit more than I'd like, but this is the minimum I could find to get node 14 in
 2021-11-23 11:43:57 +01:00
Simon Li 3b02cc4702 Run freeze.py 2021-11-19 16:49:45 +00:00
YuviPanda 27399081ff Merge remote-tracking branch 'upstream/main' into no-node 2021-11-19 22:00:10 +05:30
YuviPanda 6db7273423 Revert "Freeze new environment.yaml files" 
This just causes a lot of merge conflicts

This reverts commit 6d1dc4a77b.
 2021-11-19 21:58:17 +05:30