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554 Commity (aa57e01d241ffbb93cb15a3d36971a9f6946170a)

Autor SHA1 Wiadomość Data
Erik Sundell 98aceac76d tests: cleanup legacy logic 
These files are no longer used as of repo2docker PR 912
 2022-11-11 07:55:45 +01:00
Erik Sundell e6a66316ab ci: update outdated comment in node test 2022-11-11 07:55:12 +01:00
Erik Sundell 9be3ac697c
Merge pull request #1216 from frankier/julia-binder-dir-project-toml 
Create Julia projects based on binder/Project.toml when found
 2022-11-09 17:40:10 +01:00
Erik Sundell 37ce79a5d4
Merge pull request #1211 from minrk/cli-defaults 
reconcile CLI/config priority
 2022-11-09 17:26:00 +01:00
Erik Sundell 430565faf7 ci: coalesce tests to avoid increasing test durations 2022-11-09 17:13:12 +01:00
Min RK 8802ca2a30
update test expectations of log messages 2022-11-08 16:28:01 +01:00
Min RK 2a9dab13f8
test some cli > config > defaults priority 
not full coverage, but covers some important cases
 2022-11-08 16:01:31 +01:00
Frankie Robertson e99a106171 Add test for Julia project.toml in binder subdirectory 2022-11-08 15:13:39 +02:00
Sylvain Corlay 3e5a64f82f Upgrade to mamba 1.0 2022-11-03 00:50:34 +01:00
pre-commit-ci[bot] ae3aeb6dc5 [pre-commit.ci] auto fixes from pre-commit.com hooks 
for more information, see https://pre-commit.ci
 2022-10-31 22:40:52 +00:00
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 757799516d
ensure some cache files are cleaned up 2022-10-31 15:23:35 +01:00
Min RK bd02e2e997
run check-tmp as root 
- avoids permission errors
- lets us check /root/ where we've left files in the past
 2022-10-31 15:22:56 +01:00
Min RK 2da784ca21
check-tmp needs to run on Python 3.5 2022-10-31 15:22:55 +01:00
Min RK 38f5aceb45
Add check-tmp step to local repo tests 
- check-tmp checks disk usage in a collection of directories,
  and fails if they exceed a certain size, reporting on contents
- re-use images and skip build stage in verify/check-tmp tests.
  Should save some time,
  even though the build cache would have been used.
  This way, we don't even check.
 2022-10-31 15:22:52 +01:00
Nicholas Bollweg 23e195f363 add path check in conda/repo-dir, more docs in conftest.py 2022-10-31 13:09:17 +01:00
Erik Sundell b3234b54f0 Refactor to f-strings to comply with pyupgrade 2022-10-31 12:57:23 +01:00
Min RK b314ba90cd test new port argument possibilities 2022-10-31 12:57:23 +01:00
Min RK e9ad8fdb41
run submodule test over https 
avoids assertion with file-based submodules
 2022-10-24 14:30:08 +02:00
Erik Sundell 1e4bc50a77 refactor readme files: in julia tests 2022-10-16 11:04:10 +02:00
Erik Sundell af076ca7de refactor readme files: in r tests 2022-10-16 11:03:48 +02:00
Erik Sundell 3ea45d1258 refactor readme files: in conda tests 2022-10-16 11:03:24 +02:00
Erik Sundell 42bb1b384a ci: adjust to and rename extra-args.yaml to test-extra-args.yaml 
I misunderstood extra-args.yaml to be a file that was recognized by
repo2docker's CLI, but in reality it was just a file recognized by the
repo2docker test suite. Following that, I renamed this testing specific
file to test-extra-args.yaml to help others avoid making that mistake
and added comments to clarify that.

This commit also gathers the conda buildpacks separate readme files into
a single readme file.
 2022-10-15 15:42:35 +02:00
Erik Sundell a6af244605 ci: refactor julia tests, from 5 to 4 (~5 min saved) 2022-10-10 11:15:56 +02:00
Erik Sundell f1b1339507 ci: refactor conda tests, from 6 to 5 (~5 min saved) 
With this commit, we combine testing the default python version
installation into the default R version installation test.
 2022-10-10 09:15:17 +02:00
Erik Sundell f69d65feb9 ci: refactor conda tests, from 11 to 6 (~20 min saved) 2022-10-10 09:15:17 +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 f8d0efe490 ci: delete julia/julialegacy_version-[1|1.1] tests (~10 min saved) 2022-10-10 09:15:17 +02:00
Erik Sundell 5ffbe65bec ci: delete conda/channel-dep test of a mamba 0.6+ feature (~5 min saved) 2022-10-10 09:15:17 +02:00
Erik Sundell 87dd7e1283 ci: delete conda/r4.0 test, where r3.6 and r4.2 remains (~5 min saved) 2022-10-10 09:15:17 +02:00
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