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729 Commity (27c2b403dbd3b6bb1b31f687ca4069434301465f)

Autor SHA1 Wiadomość Data
pre-commit-ci[bot] 27c2b403db [pre-commit.ci] auto fixes from pre-commit.com hooks 
for more information, see https://pre-commit.ci
 2022-10-31 22:32:14 +00:00
Erik Sundell 15a1fb6e2d refactor: manually add transitions to f-strings 2022-10-31 21:22:32 +01:00
pre-commit-ci[bot] 5a93542321 [pre-commit.ci] auto fixes from pre-commit.com hooks 
for more information, see https://pre-commit.ci
 2022-10-31 21:22:32 +01:00
Min RK e7c93b0fc8
update pipenv to 2022.1.8 
pipenv 2018 doesn't actually clear its cache when asked to

2021.5.29 is the last to support 2.7, 3.5
 2022-10-31 15:23:35 +01:00
Min RK 757799516d
ensure some cache files are cleaned up 2022-10-31 15:23:35 +01:00
Min RK 6b0291551d
Make sure we delete /tmp/shiny.deb 
revealed by check-tmp
 2022-10-31 15:22:55 +01:00
Erik Sundell 9a80e95600 pipfile: pass --clear flag, and do it separetely to not be ignored 
Maybe --clear flag works as part of `pipenv install` now, but code
inspection indicates to me it still don't. This resolves the issue with
the pipenv versions we currently use in tests at least.
 2022-10-31 14:54:54 +01:00
Erik Sundell 2f13af8a29 Apply suggestions from code review 2022-10-31 13:09:17 +01:00
Nicholas Bollweg df733fc81b normalize ENV syntax, combine more layers 2022-10-31 13:09:17 +01:00
Nicholas Bollweg 803a1c223b ensure existence/permissions on custom target dir, if doesn't exist, repo copy slash 2022-10-31 13:09:17 +01:00
Yuvi Panda 380f8177d0
Merge pull request #1188 from consideRatio/pr/ci-speedup 
ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min
 2022-10-17 22:09:35 -07:00
Jeremy Tuloup f572c3a9de Update Jupyter dependencies 2022-10-13 14:43:36 +00:00
Erik Sundell a6af244605 ci: refactor julia tests, from 5 to 4 (~5 min saved) 2022-10-10 11:15:56 +02:00
Erik Sundell 2c0b14c7da ci: refactor r tests, from 8 to 5 (~15 min saved) 2022-10-10 09:15:17 +02:00
Erik Sundell 4540bf1cc9 Remove conda buildpacks pin of r-irkernel to 1.2 
If r-base is pinned, r-irkernel will resolve to a version that is
compatible with it. But if we pin r-irkernel and not r-base, the
opposite will happen and we will end up with an older version of r-base
than is supported by r-irkernel's modern versions.

I find debugging how versions resolve with conda is really tricky, so
unless we have clear principles of what the pin should be and why, I
strongly advocate we don't have it pinned here.

In this case, having r-irkernel pinned to 1.2 caused us to get stuck at
R version 4.1 instead of going to R 4.2 that is now available.
 2022-10-10 01:56:16 +02:00
Erik Sundell b3de499659
Merge pull request #1165 from yuvipanda/bump 
Bump default R version to 4.2 from 4.1, and let R 3.4 go from 3.4.0 to 3.4.4
 2022-10-09 10:06:36 +02:00
Erik Sundell 7e517cfb0a Update R 3.4 from 3.4.0 to 3.4.4 2022-10-08 14:07:00 +02:00
Erik Sundell fc08ee1c58 Update R 4.2 from 4.2.0 to 4.2.1 and fix tests 2022-10-08 14:06:29 +02:00
Min RK 1841bf7130
fail on unsupported Python 
rather than warning (which users won't see) and building with the wrong version of Python
 2022-09-06 10:22:27 +02:00
Simon Li 0f52247b93
Merge pull request #1177 from minrk/logs 
consistent log handling when not using JSON loggers
 2022-08-24 14:37:02 +01:00
Min RK 996beea228
missing f in the f-string 
Co-authored-by: Simon Li <orpheus+devel@gmail.com>
 2022-08-24 13:06:42 +02:00
Min RK 8bf808bd4c
consistent log handling when not using JSON loggers 
our logger was never being quite hooked up when not using JSON loggers,
meaning that log messages (such as those fixed here to include newlines) were never shown.
 2022-08-22 15:16:40 +02:00
Min RK cac960d10d
add Python 3.10 base environment 2022-08-22 15:09:02 +02:00
YuviPanda d6f5c95e52 bump lock files 2022-08-01 19:51:31 -07:00
YuviPanda 5738d4161c Bump version of nodejs 
16 is also an LTS, and is the current active LTS.

Triggered by code-server package needing a newer version of nodejs!
 2022-08-01 19:51:31 -07:00
Yuvi Panda e725b079da
Merge pull request #1173 from manics/freezepy-update 
Freeze.py update
 2022-08-01 16:58:52 -07:00
Yuvi Panda 42bb1a0383
Merge pull request #1171 from SylvainCorlay/update-mamba 
Update mamba
 2022-08-01 16:48:25 -07:00
Simon Li 7eff2e6c6c freeze.py: Remove `3.6` 
The 3.6 lockfile was removed in https://github.com/jupyterhub/repo2docker/pull/1149 but freeze.py wasn't updated
 2022-08-02 00:04:53 +01:00
Simon Li 671636b9f1 `freeze.py`: needs `--kind=explicit` 
See https://github.com/conda-incubator/conda-lock#pre-10-compatible-usage-explicit-per-platform-locks
 2022-08-02 00:04:11 +01:00
Sylvain Corlay 8a4c48e88f Update mamba 2022-08-01 23:03:15 +02:00
YuviPanda 0b76608208 Bump default R version to 4.2 
Been out for a bit now
 2022-07-06 16:39:15 -07:00
YuviPanda 8af47e9985 Add comment about how r_version is determined 2022-06-23 12:34:48 -07:00
YuviPanda 28035d6426 Make sure our default R version is valid semver 2022-06-23 09:14:34 -07:00
YuviPanda e51eae9287 Don't specify older patchlevel as default R 2022-06-23 03:23:47 -07:00
Yuvi Panda a098f95dc4
Point to a tagged version of rstudio 
Co-authored-by: Simon Li <orpheus+devel@gmail.com>
 2022-06-22 23:37:42 -07:00
Yuvi Panda 232dddac50
Fix typo 
Co-authored-by: Simon Li <orpheus+devel@gmail.com>
 2022-06-22 13:40:04 -07:00
YuviPanda dfa23f6306 Set custom env vars required for RStudio to work 2022-06-22 08:49:28 -07:00
YuviPanda 9d89d6bd69 Use . instead of source 
As Dockerfile executes with /bin/sh, not /bin/bash
 2022-06-22 08:49:28 -07:00
YuviPanda a9443f04fe Don't hardcode Ubuntu version when fetching R 
This allows us to dynamically change the base image
without having to manually change the version string here
 2022-06-22 08:49:28 -07:00
YuviPanda 9c335a5e9e Cleanup apt-update files after installation 2022-06-22 08:49:28 -07:00
YuviPanda ba82209e67 Remove tests that checked if specific R packages were installed 2022-06-22 08:49:28 -07:00
YuviPanda c1ce8fd189 Use apt rather than debi to install packages 
apt also seems to fetch dependencies when needed
 2022-06-22 08:49:28 -07:00
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
Ümit Seren 3ee04e34a3 Fix Read-Only filesystem permission issue for log file 2022-05-03 16:05:55 +02:00