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572 Commity (09f3d533670da2aeff6bdc1e2e08c96fab769bd4)

Autor SHA1 Wiadomość Data
Erik Sundell b18adce53f ci: test conda/py310 instead of conda/py38 2022-10-10 09:15:17 +02:00
Erik Sundell 3034a09a91 ci: test conda/r4.2 instead of conda/r4.1 2022-10-10 09:15:17 +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 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
YuviPanda d695b3dcdf Bump npm version too 2022-08-01 19:51:31 -07:00
YuviPanda be39a1a3f2 Bump up test for nodejs version 2022-08-01 19:51:31 -07:00
Yuvi Panda 42bb1a0383
Merge pull request #1171 from SylvainCorlay/update-mamba 
Update mamba
 2022-08-01 16:48:25 -07:00
Sylvain Corlay 8a4c48e88f Update mamba 2022-08-01 23:03:15 +02:00
YuviPanda b97db1066d Fix indexes in tests that look for staging zenodo 2022-07-28 10:02:10 -07:00
YuviPanda 0b76608208 Bump default R version to 4.2 
Been out for a bit now
 2022-07-06 16:39:15 -07:00
YuviPanda 8ed4c96a8e Put simple test date back to where it was 
Let's remove unnecessary changes
 2022-06-22 16:20:58 -07:00
YuviPanda 2819a6d1b4 Upgrade simple to a newer r snapshot 
2020 had an older version of testthat that ran into issues

> # Error in get(genname, envir = envir) : object 'testthat_print' not found
 2022-06-22 08:49:28 -07:00
YuviPanda 9fa096d0f6 Don't specify distro specific build number 2022-06-22 08:49:28 -07:00
YuviPanda def4009a6b Remove another unneeded R unit test 
We want users to be able to install new versions of R
as soon as they are out, without us having to do anything
special in repo2docker. So we can't actually check for 'invalid'
R versions. This is ok, as we don't have to special case apt repos
or similar when installing R from rstudio's debs
 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
Dara Adib 56bf03811e Add test for shallow clone HEAD 2022-06-02 20:54:43 -04:00
YuviPanda 672c21ff82 Make black happy 2022-04-08 13:55:06 -07:00
Min RK 5cfd798008 handle r version unspecified in environment.yml 2022-02-25 12:03:40 +01:00
Simon Li c83efb0427
Merge pull request #1130 from minrk/bump-python-docker 
update Python in some dockerfile tests
 2022-02-12 14:58:44 +00:00
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
Min RK f2f8bb666e update Python in dockerfile tests 
installing with Python 3.5 is starting to fail
 2022-01-28 15:48:55 +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
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
Min RK 8ab5c81245 remove deprecated call to distutils strtobool 2022-01-26 09:56:15 +01:00
Simon Li 813d28bfdb
Merge pull request #1115 from minrk/set-user-root 
set USER root after each directive block
 2022-01-25 14:55:11 +00:00
YuviPanda 9066d079d0 Use testthat, rather than tinytest 
tinytest doesn't exist in older MRAN snapshots
 2022-01-25 19:38:47 +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
YuviPanda f6737cfff5 Use a smaller R library in our tests 
ggplot2 is a big library with a bunch of dependencies,
making our already slow R tests even slower. This PR
switches them to using the tinytest library, which has
no dependencies and is much smaller.
 2022-01-25 18:58:58 +05:30
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 5f82b2c8b0 Update micromamba installation 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 7c4f2a5b4f fix up urls 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 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 2bfbf44efa adhere to lint 2022-01-21 11:21:00 +01:00
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
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
Andrei Plamada 8a817eba97 add tests for R conda 2022-01-07 13:37:43 +01:00
YuviPanda 3cb3fbf853 Remove unnecessary print() 2022-01-07 11:18:09 +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 7c36566bf2 Fix test for particular version of R 3.6 2022-01-05 01:24:10 +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 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 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
YuviPanda 054b602b13 Add test for r3.6 2021-12-20 18:24:15 +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 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
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
YuviPanda 730e622e3f Support R 4.1 2021-12-16 12:16:52 +05:30
Anton Akhmerov 8db656d1ce
always unpack a single zenodo zip 2021-07-06 15:18:42 +02:00
Simon Li 4ed6685dc9 Fix unit tests 2021-07-02 12:43:58 +01:00
Simon Li 9ac8a8314c Handle attrs["State"]["ExitCode"] 2021-07-02 12:42:10 +01:00
Mridul Seth 3edc76342c Fix regression in hydroshare introduced after moving to requests 2021-04-01 15:31:19 +02:00
Tim Head 8731ecf096
Merge pull request #1014 from minrk/flush-buffers 2021-03-23 07:21:00 +01:00
Min RK ebf640cb84 implement entrypoint in Python 
- make sure to set PYTHONUNBUFFERED
- implement tee with subprocess readlines
- forward all relevant signals from entrypoint to 'true' command
- add monitor process to ensure child shuts down if parent does (maybe not useful in docker?)
 2021-02-17 16:13:42 +01:00
Yuvi Panda f426891014
Merge pull request #960 from minrk/r4 2021-02-17 17:53:53 +05:30
Min RK e862630ee1
Merge pull request #1008 from betatim/missing-logs 
Investigating the missing logs
 2021-02-17 10:23:11 +00:00
Mridul Seth 0885204a5d fix dataverse regression introduced in last release 2021-02-11 21:58:21 +01:00
Tim Head 6e372b5bc9 Extreme measures 2021-01-28 09:17:34 +01:00
Simon Li cb4621f254
Merge pull request #987 from betatim/stream-logs 
[MRG] Stream jupyter server logs to a file
 2021-01-27 17:08:17 +00:00
Tim Head 1140dd1919
Merge pull request #988 from douardda/swhid 2021-01-26 13:56:29 +01:00
Tim Head 45229ad613
Merge pull request #1001 from manics/fix_figshare_test 2021-01-20 11:20:13 +01:00
David Douard e54c24ce2e Add support for the SWHID content provider 
This content provider allows to retrieve the content from a
Software Heritage (SWH) persistent identifier (SWHID).
Typical usage:

  repo2docker swh:1:rev:94dca98c006b80309704c717b5d83dff3c1fa3a0

It uses the SWH public vault API to retrieve the content of the given
directory.

Most of the times, this will not need an authentication
token to bypass the rate-limiting of the SWH API.
Without authentication, one should be allowed to retrieve one
directory content per minute.

If this is not enought, then the user must use authenticated calls to
the SWH API.

For this, a new `swh_token` config item has been added to the Repo2Docker
application class.

To use authentication:

  repo2docker --config cfg.json swh:1:rev:94dca98c006b80309704c717b5d83dff3c1fa3a0

with the swh_token config option being defined in the cfg.json config file.
 2021-01-19 18:04:46 +01:00
Tim Head a0606f2b57
Merge pull request #993 from douardda/requests 
Replace urllib by requests in contentproviders
 2021-01-19 17:51:00 +01:00
David Douard 830a9c89c0 Replace urllib by requests in contentproviders 
requests is globally simpler to use, and more and more people
are more familiar with this later than urllib.
 2021-01-18 17:29:53 +01:00
Tim Head c75b5ab72a
Merge pull request #990 from FRidh/nix 
buildpacks/nix: disable sandboxing (bugfix)
 2021-01-17 10:00:20 +01:00
Simon Li 5e6aa2aa9b Mark failing figshare tests as xfail 2021-01-09 11:36:12 +00:00
Simon Li bcc97a2382 Bug in figshare? 
It looks like the new figshare redirects may drop the version suffix causing two tests to fail (see the test comments).
 2021-01-08 23:48:58 +00:00
Frederik Rietdijk 5c4c2dc40e buildpacks/nix: disable sandboxing 
The version bump #915 broke the Nix buildpack in case one does a build.

Nix 2.3 enables sandboxing by default. Building inside a Docker
container, while Nix is having sandboxing enabled is not possible. Thus,
sandbox = false should be set in /etc/nix/nix.conf.
 2020-12-19 09:31:04 +01:00
Sylvain Corlay 6c1a2722b9 Use mambaforge instead of miniforge 2020-12-06 11:50:11 +01:00
Tim Head f2ed09bdfb Ensure output arrives on stderr 2020-11-26 14:53:31 +01:00
Jeremy Tuloup 53a9071e5e Update to node 14 2020-11-20 09:38:44 +01:00
Min RK edfca79371 Remove support for stencila 
Changes in stencila mean it doesn't work anymore and it's not feasible to update nbstencilaproxy

Instead, show only a warning about removed support for stencila
 2020-11-19 18:17:23 +01:00
Simon Li 30ef2209cc
Merge pull request #979 from minrk/mamba-061 
Mamba 0.6.1
 2020-10-23 09:58:48 +01:00
Min RK 1bb92770eb regression test for specifying channel name in enviornment.yml dependency 
this didn't work with mamba 0.5
 2020-10-22 15:30:31 +02:00
Kyungdahm Yun 81513b06d6 Add test for writable permission on REPO_DIR 2020-10-19 21:49:09 -07:00
paugier 05002a4177 hg-evolve required for Mercurial support (simpler) 2020-09-14 14:05:52 +02:00
Min RK dd3fa631dd support R 4 2020-09-14 11:55:52 +02:00
paugier 39081b70c3 Fix bug hg id topic 2020-09-11 00:36:28 +02:00
paugier 64633bbcbc Documentation about Mercurial support 2020-09-11 00:10:55 +02:00
paugier 3cdde89328 By default run Mercurial tests + enable the topic extension from code (no need for config file) 2020-09-10 21:48:46 +02:00
paugier 5bb586931b Mercurial optional 2020-09-10 07:58:21 +02:00
paugier c91ed4eec5 Mercurial: remove conditions for py3.5 + requirements only in setup.py 2020-09-08 10:09:13 +02:00
paugier fc3cef16a1 Fix test_mercurial.py (black, node_id and git->hg) 2020-09-07 09:51:30 +02:00
paugier 2d2e9bf19a Skip Mercurial for Python 3.5 2020-09-07 09:38:07 +02:00
paugier e520b900bf Add a Mercurial contentprovider 
MyBinder could support Mercurial repositories

See https://github.com/jupyterhub/binderhub/issues/1148
 2020-09-04 15:14:04 +02:00
Min RK 5179447aea
Merge pull request #928 from gesiscss/configdirtest 
little improvement for testing binder_dir
 2020-08-17 10:24:10 +02:00
Tim Head 4e3016981d Unrecognised and invalid lines don't disable optimisation 
Lines in requirements files that we don't recognise or are syntax errors
do not disable our "optimised" build process.
 2020-08-17 08:01:20 +02:00
Tim Head a7ab636441 Add additional test cases and robuster parsing 2020-08-13 14:29:50 +02:00
Tim Head 6d2b129ed8 Handle requirements.txt with `--pre` lines 
This is a global flag which our inspection of requirements.txt files
should ignore as it doesn't imply a local reference.
 2020-08-13 14:00:16 +02:00
Min RK 60555b1d05 update repo URLs for jupyterhub/repo2docker 2020-08-10 09:33:05 +02:00
Tim Head f5a7711af5 Update snapshot date for simple R test 2020-07-30 16:37:29 +02:00
Tim Head fc9891b541 Upgrade custom test infrastructure for pytest 6.0.0 2020-07-30 15:15:56 +02:00
Simon Li 72fbd65649 validate_image_name: mention lowercase, fix formatting 2020-07-27 20:32:34 +01:00
Kenan Erdogan 00ec28441d merge similar test cases and use equal instead of in 2020-07-08 17:58:30 +02:00
Tim Head df77a99ce1 Make the memory limit test simpler 
Instead of checking that a build which allocates too much memory does
fail, we now only check that we pass the correct arguments to the Docker
API client. It seems reasonable to rely on the docker client working and
doing the right thing. This solves a problem where our CI is flakey
because the kernel of the VM the tests run on doesn't support this.
 2020-06-12 19:03:48 +02:00
Tim Head bbc3ee02c0
Merge pull request #882 from hwine/GH-881_make_macOS_docker_work 2020-04-27 16:20:20 +02:00
Hal Wine 69f4663700 Fix test_env.py 
This works around an issue where the temp directory can not be added to
Docker. In this case, the directory is immediately deleted, and does not
occupy significant disk space. There should be no impact to the move.
 2020-04-22 21:33:13 -07:00
Hal Wine a09e523fd4 Expand test cases to cover current Docker handling 
Examination of docker's handling showed a few additional cases were
needed.
 2020-04-19 16:44:06 -07:00
Hal Wine 6f59fdb20f Refactor to eliminate need for volume mount 
This change allows, imo, the test to be clearer, and should also speed
up the test.
 2020-04-19 16:41:11 -07:00
Hal Wine af5d9c7129 Add failing test for bare env argument value 2020-04-18 09:59:35 -07:00
Tim Head 27bca4a351 Add reported failing spec 2020-03-27 15:32:00 +01:00
Tim Head 110d34d041 Improve handling of pip arguments when detecting local dependencies 2020-03-27 15:28:19 +01:00
Tim Head 5ef65f9806 Formatting changes only 2020-03-27 15:15:14 +01:00
YuviPanda 798ba4f4bd Fix conda test to account for newer conda 2020-03-04 22:12:38 +05:30
Tim Head 26542dfc85
Merge pull request #851 from manics/mran-latest 
[MRG] If looking for latest MRAN URL try earlier snapshots too
 2020-02-24 10:19:09 +01:00
Simon Li 6a07a48b2d Test R latest MRAN date handling 2020-02-22 11:29:59 +00:00
Simon Li 39f6fc2790 unit test for utils.execute_cmd no EOL 2020-02-16 14:26:54 +00:00
Chris Holdgraf 900d280561
[MRG] add Hydroshare as a content provider (#800) 
[MRG] add Hydroshare as a content provider
 2020-02-03 10:52:48 -07:00
Tim Head 356ea10868
Merge pull request #840 from minrk/py38 
Python 3.8 support
 2020-01-30 16:10:37 +01:00
Min RK 7d20da1d04 add test for py38 2020-01-30 11:53:16 +01:00
Uwe L. Korn 5421e09d2b Make tests/conda/r/verify excutable 2020-01-30 10:51:47 +01:00
Uwe L. Korn ffbc7c0a6b Add tests for r-in-conda 2020-01-30 08:15:42 +01:00
Scott Black 02d0107510 Merge remote-tracking branch 'upstream/master' into hydroshare-content-provider 2020-01-29 10:14:01 -07:00
Min RK a337ee8020 update node10 test to reflect the removal of conda nodejs 2020-01-29 16:38:24 +01:00
Tim Head 4598a08ff9 Remove a test of legacy buildpack 2020-01-25 07:42:14 +01:00
Tim Head 9cfdb9b5f4 Add test for deprecated legacy buildpack 
Tests that the legacy buildpack raises exceptions when it is triggered.
 2020-01-25 07:35:00 +01:00
Scott Black 0c15cb1251 cleanup tests and formatting 2019-12-07 13:34:49 -07:00
Scott Black cb7bb0bb43 remove test parameterization and use fix regex match 2019-12-06 17:36:50 -07:00
Scott Black 776d538689 update tests and code to follow best practices pointed out in review 2019-12-06 16:31:59 -07:00
David Brochart 56e6c116f3 Add test 2019-11-05 18:01:06 +01:00
Scott Black d657453b3f update hydroshare version fetch to assume timestamp is in utc 2019-10-01 11:16:34 -06:00
pughdr d64f050d34 Bumped conda version to 4.7.12 2019-10-01 11:25:10 +03:00
Scott Black dddc45acfb reformatting with lint 2019-09-30 13:50:24 -06:00
Scott Black 21e61f3099 add hydroshare resource versioning and raise exception fetch fails 2019-09-25 14:37:19 -06:00
Scott Black d89f3a66aa update hydroshare content provider to doi and add tests 2019-09-25 09:59:44 -06:00
Tim Head bfbec349c2
[MRG] Add support for installing different versions of R (#772) 
[MRG] Add support for installing different versions of R
 2019-09-18 08:15:11 +02:00
Kacper Kowalik (Xarthisius) 4df4fd6ab4
Download individual files instead of zip bundle 2019-09-17 15:44:56 -05:00
Kacper Kowalik (Xarthisius) a2f8228b15
Match DV hosts based on netloc instead of url 2019-09-16 15:03:12 -05:00
Kacper Kowalik (Xarthisius) 8edafd0d07
Add tests 2019-09-13 13:42:41 -05:00
Daniel Nüst a40e1799bd fix content_id for Figshare 2019-09-11 13:45:16 +02:00
Daniel Nüst f1ec646d2e add support for Figshare versions > 9 2019-09-11 13:18:20 +02:00
Daniel Nüst 698b8a1d7e try to improve test coverage 2019-09-11 13:17:48 +02:00
Daniel Nüst b2b75600c0 handle versions in Figshare properly 2019-09-09 08:37:02 +02:00
Daniel Nüst b2b6030492 initialize hosts as instance variable 2019-09-08 21:39:48 +02:00