Yuvi Panda
380f8177d0
Merge pull request #1188 from consideRatio/pr/ci-speedup
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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
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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
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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
Simon Li
1735925116
Use enum to standardise `phase`
2022-10-03 22:49:22 +01:00
Min RK
1841bf7130
fail on unsupported Python
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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
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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
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Co-authored-by: Simon Li <orpheus+devel@gmail.com>
2022-08-24 13:06:42 +02:00
Simon Li
c5246cd963
Merge pull request #1175 from minrk/3.10
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add Python 3.10 base environment
2022-08-23 23:47:54 +01:00
Min RK
8bf808bd4c
consistent log handling when not using JSON loggers
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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
2af4d3d46b
explicitly build linux/amd64 images
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our base-env setup assumes amd64, so avoid platform issues on e.g. ARM
2022-08-22 15:12:53 +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
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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
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Freeze.py update
2022-08-01 16:58:52 -07:00
Yuvi Panda
42bb1a0383
Merge pull request #1171 from SylvainCorlay/update-mamba
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Update mamba
2022-08-01 16:48:25 -07:00
Simon Li
7eff2e6c6c
freeze.py: Remove `3.6`
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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`
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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
ffdf544ee4
Support pulling from zenodo sandbox too
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Test uploads should go to the sandbox, rather than to
main zenodo. The installation is exactly the same.
2022-07-27 17:40:14 -07:00
wilhelmfrank
d97e32b433
Add MPDL Dataverse
2022-07-20 08:48:17 +02:00
YuviPanda
0b76608208
Bump default R version to 4.2
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Been out for a bit now
2022-07-06 16:39:15 -07:00
Erik Sundell
ae8ed290b9
Merge pull request #1161 from yuvipanda/another-r
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Get R from RStudio provided apt packages (.deb files)
2022-07-01 07:27:19 +02:00
Aaron Curtis
cae431d115
Add JPL Dataverse
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NASA's Jet Propulsion Laboratory recently implemented a dataverse installation and would like to be able to use it with repo2docker / binderhub
2022-06-28 17:56:55 -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
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Co-authored-by: Simon Li <orpheus+devel@gmail.com>
2022-06-22 23:37:42 -07:00
Yuvi Panda
232dddac50
Fix typo
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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
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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
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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
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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
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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
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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
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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
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[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
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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
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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