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Autor SHA1 Wiadomość Data
Simon Li 5778ed0381 docker.py: remove workaround for old black 2021-07-02 12:43:58 +01:00
Simon Li e32c7b02df describe ContainerEngine volume and port formats 2021-07-02 12:43:58 +01:00
Simon Li 0e7e0f003e Use standard-ish image_inspect format 2021-07-02 12:43:58 +01:00
Simon Li 5c2c8f7385 Python 3.5: can't have trailing , in function arg list (again) 2021-07-02 12:43:52 +01:00
Simon Li 52b672a17a Docker: print helpful message if daemon not running 2021-07-02 12:43:18 +01:00
Simon Li 4647dd0702 Container .build .run need to support **kwargs 2021-07-02 12:43:18 +01:00
Simon Li ad5701dd3a Remove unnecessary import 2021-07-02 12:43:18 +01:00
Simon Li 00df21069e ContainerEngine .build .push default to returning strings (stream) 2021-07-02 12:43:18 +01:00
Simon Li 8215f0b065 Remove commented engine.py code 2021-07-02 12:43:18 +01:00
Simon Li 17af0c7293 BuildError only takes positional params 2021-07-02 12:43:18 +01:00
Simon Li 4a06ef19d9 ContainerEngine is now LoggingConfigurable 2021-07-02 12:43:18 +01:00
Simon Li a73595ce4c Require image info in a fixed format 2021-07-02 12:43:18 +01:00
Simon Li 787d1d3aeb Container engine is an entrypoint: repo2docker.engines 2021-07-02 12:43:15 +01:00
Simon Li b6bead74cd Python 3.5: can't have trailing , in function arg list 2021-07-02 12:42:12 +01:00
Simon Li c521c3c950 Remove constant docker args 2021-07-02 12:42:12 +01:00
Simon Li 9ac8a8314c Handle attrs["State"]["ExitCode"] 2021-07-02 12:42:10 +01:00
Simon Li 2864b692ef app: use DockerEngine 2021-07-02 12:39:42 +01:00
Simon Li 0610edfc20 Add docker implementation of abstract engine 2021-07-02 12:39:42 +01:00
Simon Li cf35f51a38 Add abstract interface for container engines 2021-07-02 12:39:42 +01:00
Mridul Seth 3edc76342c Fix regression in hydroshare introduced after moving to requests 2021-04-01 15:31:19 +02:00
Kyungdahm Yun ebbb83b665
Set default Julia version to 1.6 2021-03-25 09:22:59 -07:00
Tim Head 8731ecf096
Merge pull request #1014 from minrk/flush-buffers 2021-03-23 07:21:00 +01:00
Min RK 71eb8058c7
Merge pull request #994 from tomyun/julia-versions 
[MRG] Fetch available Julia versions from hosted json
 2021-03-12 13:07:58 +01:00
Min RK b36a6a75f5 simplify python entrypoint 
- remove redundant monitor sibling process
- use python3-login executable instead of login shell subprocess
  (same effect, but in more natural order)
- use non-blocking binary IO in tee instead of readline
  (switch to binary mode, as text wrappers don't support non-blocking mode
   see https://bugs.python.org/issue13322)
 2021-03-09 10:45:47 +01:00
Min RK 03d673b096 support separate pip requirements.txt in base env 
- require base env to be a lockfile, environment.yml no longer allowed
- separate `requirements.py-x.y.txt` can be processed post-install, if present
- use this for Python 3.5 env, which has some dependencies only from pip (newer versions than the last py35 build on conda-forge)
 2021-03-08 12:58:14 +01:00
Min RK 789a3a23c3 lockfiles need to be installed with `conda create` not `conda env create` 
use different .lock filename extension, following conda-lock precedent

Could also follow .txt in conda docs!

conda env create -p prefix -f lock.txt *should* work,
but fails with errors about name being required,
but also fails if name is given due to conflict with `-p`
 2021-03-03 16:03:52 +01:00
Min RK d7c26b7a79 use mamba create instead of mamba env create 
I'm never sure what the difference is,
but mamba env create doesn't accept explicit dependency format
 2021-03-03 13:17:46 +01:00
Min RK 93de3872a4 refreeze after adding pip 2021-03-03 12:09:13 +01:00
Min RK a2d0329b15 explicitly put pip in the base env 
instead of depending on conda's automatic pip dependency for Python,
which is sensitive to configuation
 2021-03-03 12:09:13 +01:00
Min RK 1e240efc96 refreeze with conda-lock 2021-03-03 11:18:47 +01:00
Min RK a49d260ac9 Freeze enviornment with conda-lock 
approximately one million times faster than running a full install

installation time should be faster, too, as there is no solve
 2021-03-03 11:18:27 +01:00
Simon Li d24d7e4645
Merge pull request #1017 from minrk/39 
freeze with mamba, add 3.9
 2021-03-03 10:02:55 +00:00
Min RK b73c96eecf refreeze with strict channel priority 
make sure we don't get any packages from 'defaults'
 2021-02-22 13:31:29 +01:00
Min RK 907c6f3ce5 freeze with strict channel priority 
avoids pulling in newer releases from defaults

this is conda's default behavior, but not mamba's
 2021-02-22 13:26:12 +01:00
Min RK 246d99c2a5 refreeze 
adds 3.9 environment
 2021-02-22 13:10:26 +01:00
Kyungdahm Yun 27a0ed870c Manually specify default compat version 1.5 2021-02-19 09:43:23 -08:00
Kyungdahm Yun 80837821ad Catch errors on fetching Julia versions 2021-02-19 09:09:53 -08:00
Kyungdahm Yun fc6ea2d53b Fetch available Julia versions from versions.json 2021-02-19 09:08:03 -08:00
Gerhard Bräunlich b66caf6f65 buildpacks.r: dont use apt-key directly to respect *_proxy env vars 2021-02-18 16:37:57 +01:00
Min RK 0f848f7855 handle $R2D_ENTRYPOINT in new entrypoint 2021-02-18 14:34:07 +01:00
Min RK 67cc5f7a75 bump notebook, nbconvert, jupyterhub 
- jupyterhub-singleuser==1.3.0
- nbconvert==6.0.7
- notebook==6.2.0
 2021-02-18 14:25:47 +01:00
Min RK 5a32cc4ad8 refreeze with mamba, add 3.9 to freeze list 2021-02-18 14:25:47 +01:00
Min RK f8d386a596
Merge pull request #996 from jtpio/lab-3 
Update to JupyterLab 3.0
 2021-02-18 10:46:55 +00:00
Min RK a06991de50 entrypoint needs to run on py35 2021-02-18 09:46:42 +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
Jeremy Tuloup 4c061eebbb Update to jupyter-offlinenotebook=0.2.1 2021-02-16 15:55:27 +01:00
Jeremy Tuloup 0ca6b4388a Update to jupyterlab==3.0.7 and ipywidgets=7.6.3 2021-02-16 15:22:26 +01:00
Jeremy Tuloup 37c7f5a379 Update to jupyterlab==3.0.4 2021-02-16 14:54:38 +01:00
Jeremy Tuloup e0432d37e7 Update to jupyter-offlinenotebook==0.2.0 2021-02-16 14:54:38 +01:00
Jeremy Tuloup bd08989717 Add jupyter-offlinenotebook 2021-02-16 14:54:38 +01:00
Jeremy Tuloup bcce6e8a1e Update to JupyterLab 3.0 2021-02-16 14:54:38 +01:00
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
David Douard 983607fed7 Fix the docker image name generation 
make sure all the parts that constitute the generated docker image name
are escaped, otherwise the docker building process can fail (with a rather
hard to understand error).

Before this fix, the `provider.content_id` was not escaped.
 2021-01-19 18:03:50 +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 ee7f7790d3 figshare article types: code and dataset 2021-01-15 16:11:27 +00:00
Tim Head b464a5e400
Merge pull request #991 from FRidh/nix-2.3.9 
buildpacks/nix: 2.3 -> 2.3.9
 2021-01-13 11:16:06 +01:00
Simon Li b032ad7c4b Can't just use '([^/]+)/' for the new figshare url 
This may break detection of non-code URLs
 2021-01-08 23:46:57 +00:00
Simon Li c33840fa16 Allow extra path in figshare URLs 
Copied from 1d818e90ca
 2021-01-08 23:29:37 +00:00
Frederik Rietdijk 76444c2351 buildpacks/nix: 2.3 -> 2.3.9 
Update to latest version.
 2020-12-19 09:31:55 +01:00
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 d8a3d7fa0a Update mamba to latest 2020-12-08 11:23:21 +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
Tim Head 044e112bae Explicitly close log output 2020-11-26 13:01:07 +01:00
Tim Head 957571f739
Add StackOverflow link to comment 
Co-authored-by: Simon Li <orpheus+devel@gmail.com>
 2020-11-26 07:27:06 +01:00
Tim Head 3dd2b8652d Stream jupyter server logs to a file 
By streaming the logs also to a file users can access them from inside
the container which helps them debug issues without having to ask an
admin.
 2020-11-25 13:27:11 +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
Kyungdahm Yun 4ca664320d
Add Julia 1.5.3 support 2020-11-10 11:16:42 -08:00
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 e4b1779999 mamba 0.6.1 2020-10-22 15:29:16 +02:00
Tim Head 1ebb4b5d87 Add explicit error message when `master` is specified 
Provide a specific error messaeg with a hint towards solution
when a user specifies `master` as ref and we can't find it.
 2020-10-22 08:04:29 +02:00
Tim Head 19c698e8d3 Remove reference to `master` branch from CLI doc 2020-10-22 07:46:20 +02:00
Kyungdahm Yun 8f714b48be Ensure REPO_DIR owned by NB_USER 2020-10-18 00:39:49 -07:00
Nicholas Bollweg 778c914c8c use jinja var for COPY chown 2020-10-15 08:58:12 -04:00
Nicholas Bollweg dc559b825a add chown to COPY commands to reduce layer count 2020-10-14 23:18:18 -04:00
Tim Head ae6c2dc8b9
Merge pull request #965 from tomyun/patch-2 
Add Julia 1.5.2 support
 2020-09-25 14:36:25 +02:00
Simon Li 369b57c794
conda: set TIMEFORMAT for timed bash commands 2020-09-24 19:11:48 +01:00
Kyungdahm Yun 78adb93837
Add Julia 1.5.2 support 2020-09-24 00:00:59 -07:00
Sylvain Corlay 908bc0f8ff One more time (pun intended) 2020-09-21 15:06:21 +02:00
Sylvain Corlay 56fb7e8160 missing -y 2020-09-21 14:22:51 +02:00
Sylvain Corlay 3e07ba2fa5 Fix shell syntax error with time 2020-09-21 14:22:51 +02:00
Sylvain Corlay 916a03f1d5 Update mamba 2020-09-21 14:22:51 +02:00
Min RK 6f9a523b76 install conda packages with mamba 
might save us some time

adds timing measurement to most of the commands that take a while,
not sure if we want to keep that
 2020-09-21 14:22:51 +02:00
Tim Head 35e6e7eda6
Merge pull request #950 from paugier/mercurial-contentprovider 2020-09-21 08:47:21 +02:00
Simon Li 45eccfe7f6 Disable jupyterlab extension build minimize 2020-09-18 10:51:39 +01:00
Min RK dd3fa631dd support R 4 2020-09-14 11:55:52 +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 fadb3c8dc8 Bump Black version (20.8b1) and use --target-version=py36 2020-09-10 08:11:29 +02:00
paugier 5bb586931b Mercurial optional 2020-09-10 07:58:21 +02:00
paugier 96914545e1 Update Dockerfile (ALPINE_VERSION=3.12.0 & install mercurial) + remove mercurial from install_requires 2020-09-09 18:10:19 +02:00
paugier 979c4abe00 Add Mercurial in content_providers in repo2docker/app.py 2020-09-07 10:06:58 +02:00
paugier d26b3dd0df Mercurial: use the full node id (12 characters) for the content_id 2020-09-07 09:43:22 +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
Kyungdahm Yun 23dd20b341
Add Julia 1.5.1 support 2020-09-02 11:01:50 -07:00
Min RK 6b8f5cf5e8
Merge pull request #943 from betatim/better-requests-parsing 
[MRG] Handle requirements.txt with `--pre` lines
 2020-08-17 10:22:51 +02:00
Tim Head 10a0cdd04b Smarter splitting without try/except 2020-08-17 08:06:08 +02:00
rkevin ce17956601 add www-frame-origin=same to /etc/rstudio/rserver.conf 2020-08-14 06:27:53 -07:00
Tim Head 82eb2b1903
Merge pull request #938 from tomyun/patch-1 
Add Julia 1.5.0 support
 2020-08-14 11:22:56 +02:00
Tim Head a7ab636441 Add additional test cases and robuster parsing 2020-08-13 14:29:50 +02:00
Tim Head 37cee9a076
Merge pull request #924 from minrk/collections.abc 
avoid deprecated import of collections.abc
 2020-08-13 14:12:47 +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
Kyungdahm Yun 64a948a03d
Add Julia 1.5.0 support 2020-08-04 10:24:06 -07:00
Tim Head 163718b277
Merge pull request #933 from manics/jupyterlab==2.2.0 
Update JupyterLab to 2.2.0
 2020-07-28 20:30:52 +02:00
Simon Li 72fbd65649 validate_image_name: mention lowercase, fix formatting 2020-07-27 20:32:34 +01:00
Simon Li e5ef9b3450 jupyterlab==2.2.0 2020-07-25 18:29:12 +01:00
Min RK c87f642acf avoid deprecated import of collections.abc 
deprecated since 3.3, due to be removed in 3.9
 2020-07-02 12:57:17 +02:00
John D. Boy 4ff6975716 Bump nix version to 2.3 
- This addresses issue #911
- This is untested, but there is no documented reason why repo2docker
  should stick with the previously pinned version 2.1.1
- Upstream has switched from bz2 to xz, so `tar` now takes the `-J` flag
  instead of `-j`
 2020-06-16 11:35:09 +02:00
Simon Li 1701771ad9
Python 2.7 wcwidth==0.1.9 
Later versions of wcwidth require `backports.functools-lru-cache>=1.2.1; python_version < "3.2"` but the conda-forge wcwidth package was automatically bumped without this new requirement.
 2020-06-03 21:38:33 +01:00
Simon Li f9862cc2c1
nbresuse==0.3.3 full freeze.py 2020-06-02 19:18:20 +01:00
David Anthoff 184bc12a1c Add Julia 1.4.2 support 2020-05-25 13:45:29 -07:00
Tim Head 8b6224999d
Merge pull request #886 from danlester/master 2020-05-15 15:43:51 +02:00
Tim Head 81e1e39b7a
Merge pull request #892 from betatim/bump-irkernel 2020-05-15 14:42:17 +02:00
Tim Head 26ce1899dc Fix RShiny proxy 
The Shiny proxy was split out of the rstudio proxy package. This meant
that RStudio sessions were still being proxied but Shiny sessions not.
 2020-05-11 11:41:32 +02:00
Tim Head c01bdf0130 Bump version of irkernel for R 4.0 2020-05-10 21:46:17 +02:00
Dan Lester 146db2f4f0 Only chmod u+x if not already executable, in case user is not owner but file is already g/o+x 2020-05-01 13:35:17 +01:00
Dan Lester 057c837a75 chmod start script from repo2docker-entrypoint 2020-04-29 18:48:10 +01:00
Tim Head 175b9308e8
Merge pull request #874 from hwine/GH-871_fix_env_option 2020-04-23 06:55:05 +02:00
Simon Li f1cd7c0af7
pypi jupyter-offlinenotebook==0.1.0 2020-04-20 10:20:30 +01:00
Hal Wine d9bf9d1a9b --env handling now consistent with Docker 
Added a custom action handler for '-e' and '--env' so that the
'environment' variable passed to docker reflects how docker would have
processed the same args
 2020-04-19 16:44:48 -07:00
Hal Wine 2c9027eb80 Change location & type of fix 
The initial plan was to modify our copy of the environment variables as
set via cli argparsing at the point-of-use. However, that function's
purpose is to launch a container.  Adding argument processing doesn't
feel right.

The new plan is to modify our copy of the environment when the arguments
are parsed. `argparse` provides a hook to do such work: custom actions.
 2020-04-18 10:29:10 -07:00
Tim Head 260774b9d2
Merge pull request #878 from davidanthoff/julia-1.4.1 2020-04-18 00:20:01 +02:00
David Anthoff 94adf0f3c7 Work around a Julia bug 2020-04-17 12:47:51 +02:00
David Anthoff 291e5d93e0 Add support for Julia 1.4.1 2020-04-17 12:46:13 +02:00
Hal Wine 54c44fcb23 Placeholder for work to come. 2020-04-15 20:49:56 -07:00
David Anthoff f050805bf0 Add support for Julia 1.4.0 2020-04-08 15:19:46 -07:00
Erik Sundell d366af9a51
Merge pull request #869 from betatim/update-server-proxy 
[MRG] Update server proxy and rsession proxy
 2020-04-05 00:22:46 +02:00
Erik Sundell 1900878302
Update repo2docker/buildpacks/_r_base.py 2020-04-04 21:36:46 +02:00
Tim Head 8b5b55732a Update server proxy and rsession proxy 
Both haven't been updated in a long time (~1yr) so we should refresh
them. This brings both to the latest commit in their repos.
 2020-04-04 15:05:00 +02:00
Tim Head 110d34d041 Improve handling of pip arguments when detecting local dependencies 2020-03-27 15:28:19 +01:00
Yuvi Panda 03ec3fe803
Make defaults channel be lower priority than conda-forge 
Co-Authored-By: Isuru Fernando <isuruf@gmail.com>
 2020-03-05 05:44:02 +00:00
YuviPanda 59684d0cbe Add defaults channel back 2020-03-05 11:02:52 +05:30
YuviPanda cc54383160 Don't explicitly try to upgrade conda 
Unlike miniconda, miniforge is likely to be updated more
often (one hopes), so we don't have to install then upgrade
conda specifically
 2020-03-04 22:13:30 +05:30
YuviPanda cbab4eaf43 Replace reference to md5 with reference to sha256 2020-03-04 15:02:34 +05:30
YuviPanda 0d0a2f8eb9 Use miniforge instead of miniconda to get conda 
[miniforge](https://github.com/conda-forge/miniforge) is a new
community-led installer that uses conda-forge as the default
channel, rather than defaults. This gives us a few advantages:

- No mixing of defaults & conda-forge channel by default. My
  intuition is that this will reduce image size & build times,
  but I don't know enough about conda to say if this is real
- It provides installers for architectures unsupported by miniconda.
  This is particularly useful important for ARM & PowerPC, when we
  want to support those better.
- I like conda-forge, and we should do what we can to support them!
  This is a fairly easy, drop-in way to do so
- It is more likely to have newer versions of conda by default
  than miniconda
- It provides sha256 hashes for installers rather than just md5. This
  makes me personally happy

There should be no user-facing changes here as far as I can tell.

Fixes #858
 2020-03-04 14:52:34 +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 5f3fcfcf08 If looking for latest MRAN URL try earlier snapshots too 2020-02-15 16:07:48 +00:00
Simon Li 57593936f0 utils.execute_cmd flush buffer if no EOL 2020-02-14 23:19:46 +00:00
Tim Head e405d9678f Make it optional to install the extension for lab 
Some versions of lab used by repo2docker are not compatible with the
offlinenotebook extension. We try to install the extension and if it
fails we move on without raising an error.
 2020-02-06 07:46:43 +01:00
Tim Head c340f4a44e Install jupyter-offlinenotebook extension 
This adds the offlinenotebook extension to the base install. With this
users can download their notebook even after the server has gone away.
 2020-02-05 23:16:57 +01:00
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 ef9daa26e5 refreeze 2020-01-30 11:58:45 +01:00
Min RK eb80fff779 add py3.8 environment 2020-01-30 11:53:17 +01:00
Min RK acd582951b make python 3.7 the default explicitly 
rather than implicit on the last entry
 2020-01-30 11:53:16 +01:00
Min RK 4f1dcd8421 add py3.8 to freeze list 
and remove 3.5 which is no longer being refrozen
 2020-01-30 11:53:16 +01:00
Min RK fb995027de make conda install conda quick with -S 
if the version is already satisfied
 2020-01-30 11:53:16 +01:00
Min RK 697bde8273 bump miniconda version to 4.7.12 2020-01-30 11:53:16 +01:00
Min RK 2e2d1f4b32 make that jupyterhub-singleuser 
which adds the appropriate restrictions on notebook
 2020-01-30 10:05:58 +01:00
Min RK 68c867cfde use old Python environment when using old Julia environment 2020-01-30 09:58:38 +01:00
Uwe L. Korn 3d8b6118e9 Only check str dependencies 2020-01-30 07:43:57 +01:00
Scott Black 02d0107510 Merge remote-tracking branch 'upstream/master' into hydroshare-content-provider 2020-01-29 10:14:01 -07:00
Uwe L. Korn e89378aea0 Start RStudio if R is installed via conda 2020-01-29 17:48:39 +01:00
Min RK 93ee8153b0 refreeze 2020-01-29 17:47:40 +01:00
Min RK 8e0c3f8e9f update base environment 
- notebook 6
- nbconvert 5.6
- jupyterlab 1.2
- widgets 7.5
 2020-01-29 17:47:31 +01:00
Min RK 573ecc9054 use jupyterhub-base 
removes nodejs from the conda environment

node is already installed on the host
 2020-01-29 16:38:06 +01:00
Kenan Erdogan d8c6b8b34b upgrade jupyterhub to 1.1.0 2020-01-27 14:01:32 +01:00
Chris Holdgraf db9f1ff9ce
[MRG] Deprecate legacy buildpack (#829) 
[MRG] Deprecate legacy buildpack
 2020-01-26 16:58:32 -08:00
Tim Head 88b6a1f6c4
Replace deprecated with removed 
Co-Authored-By: Simon Li <orpheus+devel@gmail.com>
 2020-01-25 14:29:17 +01:00
Tim Head 1a1fd34391 Remove support files for legacy buildpack 2020-01-17 18:42:03 +01:00
Tim Head 1b2de86122 Deprecate legacy buildpack 2020-01-17 18:20:19 +01:00
Tim Head d9335cf18b
Merge pull request #831 from davidanthoff/julia-1.3.1 
Add support for Julia 1.3.1
 2020-01-09 07:52:50 +01:00
David Anthoff edc85c879a Add support for Julia 1.3.1 2019-12-31 16:29:54 -08:00
Simon Li 0046829e97 r build-pack: when using ppa install r-recommended 
Attempt at fixing https://github.com/jupyterhub/mybinder.org-deploy/issues/1308
 2019-12-29 23:41:06 +00:00
Scott Black 776d538689 update tests and code to follow best practices pointed out in review 2019-12-06 16:31:59 -07:00
David Anthoff 4ec932b1ec Add support for Julia 1.0.5 and 1.3.0 2019-12-01 10:36:27 -08:00
Tim Head ee38137aac Remove explicit checkout when ref given 2019-11-07 23:15:29 +01:00
David Brochart f440daeb8b Check out hash, not ref 2019-11-07 14:45:26 +01:00
David Brochart 908161aecb Dot gets added later 2019-11-07 13:26:26 +01:00
David Brochart 39eeb82342 Raise ValueError if not able to checkout ref 2019-11-06 09:32:08 +01:00
David Brochart 97c8bfb68f Clone and check out branch in two steps 2019-11-05 18:53:45 +01:00
David Brochart 56e6c116f3 Add test 2019-11-05 18:01:06 +01:00
David Brochart e4e9c1fdce Fix submodule check out 2019-11-05 15:10:19 +01:00
Scott Black 1257a2c910 update downloading message to include full url 2019-10-14 13:56:29 -06:00
Tim Head 0dba6111c6
Merge pull request #804 from manics/user-no-log-init 
adduser: useradd --no-log-init to reduce lastlog size
 2019-10-08 16:18:09 +02:00
Tim Head 1c0e44f459 Fix up formatting for black 2019-10-07 09:14:26 +02:00
Pablo Bernabeu 7712583a51
Added Tim's suggestions (link below) 
https://github.com/jupyter/repo2docker/pull/803#discussion_r331781100
 2019-10-06 15:09:29 +01:00
Pablo Bernabeu a4777a8d43
Update repo2docker/buildpacks/r.py 
Co-Authored-By: Tim Head <betatim@gmail.com>
 2019-10-06 15:02:27 +01:00
Simon Li 2f15586474
Update repo2docker/buildpacks/base.py 
Co-Authored-By: Tim Head <betatim@gmail.com>
 2019-10-06 11:38:36 +01:00
Simon Li 91b7d752b6 adduser: useradd --no-log-init to reduce lastlog size 
If the Docker host does not support sparse files /var/log/lastlog can be extremely large if a large UID is set. --no-log-init prevents lastlog being created.
 2019-10-05 23:45:12 +01:00
Pablo Bernabeu a7d1395a7e
Fixed packages.append and updated RStudio again 2019-10-05 19:58:37 +01:00
Pablo Bernabeu 20b7b291eb
I tried my best to install r-base-dev 
I tried installing r-base-dev as it is advised in RStudio instructions. I did it adding this package wherever r-base was already.
 2019-10-05 19:13:55 +01:00
Pablo Bernabeu 0d0824d5d5
Restored RStudio Server version to its current v. 
As explained in discussion on the pull request (#803 (comment)), I did the reverse of the last commit. I restored the RStudio Server version to its current version on Binder, and thus only left Shiny Server being updated.
 2019-10-03 18:55:34 +01:00
Pablo Bernabeu 52f43e6ed1
Restored Shiny Server version to its current v. 
As explained in discussion on the pull request (https://github.com/jupyter/repo2docker/pull/803#issuecomment-538013605), I restored the Shiny Server version to its current version on Binder, and thus only left RStudio being updated.
 2019-10-03 17:37:17 +01:00
Pablo Bernabeu 422c1d1a70
Update repo2docker/buildpacks/r.py 
Co-Authored-By: Tim Head <betatim@gmail.com>
 2019-10-02 22:12:50 +01:00
Pablo Bernabeu 11efede71d
Update repo2docker/buildpacks/r.py 
Co-Authored-By: Tim Head <betatim@gmail.com>
 2019-10-02 22:12:15 +01:00
Pablo Bernabeu f17dc8133a
Updated RStudio Server and RStudio Shiny Server 
From official sites as shown: `# Via https`...
 2019-10-02 21:19:33 +01:00
Pablo Bernabeu 7f4297f813
Update r.py 2019-10-02 20:38:42 +01:00
Scott Black 16411fc35e update formatting 2019-10-01 12:59:06 -06:00
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 3a936412af use datetime for iso parsing 2019-09-30 16:59:01 -06:00
Scott Black 8dd9b5b928 update date parser to parse hydroshare date with timezone 2019-09-30 15:57:27 -06:00
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 7fcb67f06d raise exceptions during failure and add modify date version 2019-09-25 14:00:47 -06:00
Scott Black 2508cc2104 fix _urlretrieve class method 2019-09-25 10:58:45 -06:00
Scott Black d89f3a66aa update hydroshare content provider to doi and add tests 2019-09-25 09:59:44 -06:00
Scott Black 0549577a51 Merge branch 'master' of git://github.com/jupyter/repo2docker 2019-09-24 13:37:50 -06:00
Tim Head 27eeef2c97
Merge pull request #796 from nuest/dataverse-docs 
[MRG] Add docs for Figshare and Dataverse; update Dataverse installations file formatting
 2019-09-19 22:07:04 +02:00
Tim Head 2771ea4220 Use port 80 to download GPG keys to avoid firewall problems 2019-09-18 10:01:41 +02:00
Daniel Nüst 3bdf7041dc sort and pretty print dataverse.json 
so that we can track changes and only update the lines of the files that need updating
 2019-09-18 08:54:48 +02:00
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
Tim Head 548b9c8cde
[MRG] Update nteract-on-jupyter to 2.1.3 (#794) 
[MRG] Update nteract-on-jupyter to 2.1.3
 2019-09-18 08:12:16 +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) 30375d13df
Use the persistent id from the url regardless whether it's a DOI or not 2019-09-16 14:29:47 -05:00
Kacper Kowalik (Xarthisius) 14b758d327
Improve debug logging 2019-09-16 09:17:15 -05:00
Tim Head b8dd98bd52 Update nteract-on-jupyter to 2.1.3 2019-09-13 22:28:44 +02:00
Kacper Kowalik (Xarthisius) 331a610324
Add Dataverse content provider 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
Tim Head d8c8259343 Raise exception for unsupported R versions 2019-09-08 17:19:50 +02:00
Tim Head c50983532e Use LooseVersion to compare versions instead of strings 2019-09-08 14:54:51 +02:00
Daniel Nüst e6cd4b19d9 reuse hosts definition in Zenodo tests 2019-09-08 14:51:17 +02:00
Daniel Nüst 0e4029bb8d add Figshare content provider 
moving common functions to a DoiProvider
 2019-09-08 14:51:17 +02:00
Tim Head 75c2a24c0c
Print Dockerfile to stdout when --no-build (#784) 
Print Dockerfile to stdout when --no-build
 2019-09-08 07:30:11 +02:00
Tim Head e646419e19
Merge pull request #517 from yuvipanda/help 
Provide help text for commandline arguments

Co-authored-by: Min RK <benjaminrk@gmail.com>
 2019-09-08 07:29:49 +02:00
Tim Head eae42740b6 Add tests for R version handling 2019-09-08 07:25:10 +02:00
Min RK 8e1bdd9765 only log Dockerfile at debug-level if not dry_run 
avoids double-display when using --debug --no-build
 2019-09-07 14:28:14 +02:00
Min RK e9c39e2596 respect self.log_level with json logs 2019-09-07 14:25:25 +02:00
Min RK 7f0cac84b5 print Dockerfile to stdout when `--no-build` 
Removes need to also specify `--debug` to see the dockerfile, which goes to the logs
 2019-09-07 14:25:07 +02:00
Min RK 8ef5faa2ab
Merge pull request #779 from nuest/docker_daemon_logmessage 
add explicit log message on failing Docker connection
 2019-09-07 14:07:03 +02:00
Min RK 088cf6e308 let black have its way 2019-09-07 13:34:07 +02:00
Tim Head 0b839428cc Use new way of installing bioconductor 2019-09-07 13:30:46 +02:00
Min RK 4f428c3055
Merge pull request #681 from Xarthisius/abspath_in_scripts 
[MRG] Allow absolute paths in build_script_files. Fixes #673
 2019-09-07 12:33:14 +02:00
Daniel Nüst b3f82db558 exit and show clean error message (no log) if docker connection fails 2019-09-07 12:16:41 +02:00
Min RK 2871c07cc0
Merge branch 'master' into help 2019-09-07 12:16:23 +02:00
Tim Head 37774fc288
Merge pull request #727 from minrk/full-progress 
include full docker progress events in push progress events
 2019-09-07 11:45:32 +02:00
Daniel Nüst c8cd3269c0 add explicit log message on failing Docker connection, see #774 2019-09-07 09:22:00 +02:00
Tim Head e0b1d474bd Add translation from short versions to long versions 2019-09-06 22:12:46 +02:00
Tim Head 4be9fe0731 SUpport R runtime strings that don't specify a version 2019-09-06 12:12:06 +02:00
Tim Head ef9d27ac2c Add support for innstalling different versions of R 2019-09-03 07:20:38 +02:00
GeorgianaElena 795769ee28 Removed debug print 2019-08-29 15:51:12 +03:00
GeorgianaElena 95fd0e5b81 Don't change file encoding 2019-08-29 15:13:33 +03:00
GeorgianaElena 3752fa1868 Added function to handle different file encodings 2019-08-28 16:25:12 +03:00
GeorgianaElena 5983ded5bb Upgrade IRKernel version to 1.0.2 2019-08-26 17:53:53 +03:00
pughdr 6de9bd4c69 Fixed merge conflict 2019-08-26 12:50:24 +03:00
David Anthoff 445bcb981c Add support for Julia 1.2.0 2019-08-25 21:46:23 -07:00
Scott Black ebbc9e0233 update messaging 2019-08-23 11:16:39 -06:00
Scott Black b068f8d9c1 extend wait time and cleanup messaging 2019-08-23 11:09:26 -06:00
Scott Black 970c7ece20 actually reconnect 2019-08-23 11:06:02 -06:00
Scott Black 97eee3b8c0 allow for bag creation 2019-08-23 10:56:52 -06:00
Scott Black 8817fec7ac handle traliing slash in url 2019-08-22 17:24:52 -06:00
Scott Black 9927faaafd extract from contents directory 2019-08-22 17:10:55 -06:00
Scott Black fdb92525c6 only use data/contents directory 2019-08-22 17:00:55 -06:00
Scott Black 316b1a0f34 use request.urlretrieve 2019-08-22 16:41:31 -06:00
Scott Black fc9326cbf3 add hydroshare as a content provider 2019-08-22 16:39:42 -06:00
Scott Black e04bc18248 remove unused imports 2019-08-22 16:33:25 -06:00
Scott Black 5f574d3a2c initial checkin of hydroshare content provider 2019-08-22 16:30:48 -06:00
Scott Henderson 5ea4c29b83 bump conda minor version to 4.7.10 and refreeze 2019-07-29 17:30:50 +00:00
Scott Henderson 62e10d6891 switched pip packages to conda-forge 2019-07-29 17:23:09 +00:00
Tim Head 01c785f6fc Call parent preassemble scripts methods 
Without this we don't collect the files that other build packs need to
copy them over to the container in the pre-assemble stage.
 2019-07-23 07:33:06 +02:00
Tim Head 6c5c09b62b
Merge pull request #743 from minrk/conda-env-first-again-again 
[MRG] preassembly for conda/python
 2019-07-19 10:36:15 +02:00
Min RK 930e907ac6
Update repo2docker/buildpacks/conda/__init__.py 
Co-Authored-By: Tim Head <betatim@gmail.com>
 2019-07-19 08:56:06 +02:00
Tim Head 74af2ad83c
Merge pull request #748 from minrk/pipfile-toml 
parse pipfiles to determine Python version
 2019-07-18 21:48:35 +02:00
Min RK 31da8e32b1 run chown as root 2019-07-18 17:55:38 +02:00
Min RK 8236dc8ae1 only install pipenv in preassemble 
save preassembly of pipenv for a later patch
 2019-07-18 16:25:04 +02:00
Min RK 79c2617873 parse pipfiles to determine Python version 
these are structured files, no need to use regular expressions to parse them
 2019-07-18 16:13:41 +02:00
Min RK dd6cd93585 typo in doi regexp 
must use `r` prefix when there are escapes
 2019-07-18 14:41:01 +02:00
Min RK 654be046ac set permissions on repo_dir prior to preassemble 2019-07-18 14:40:08 +02:00
Min RK 3da5543bfc check for local pip requirements in conda environments 2019-07-18 14:39:35 +02:00
Min RK 4f3f192d2f preassembly for pipfiles 2019-07-16 15:52:39 +02:00
Min RK d6e66c886d preassemble python 2019-07-16 15:52:39 +02:00
Min RK ddfd3f3464 refreeze 2019-07-16 2019-07-16 15:23:00 +02:00
Min RK 70878082f6 conda install occurs in preassemble 2019-07-16 09:02:35 +02:00
Min RK 5b12e072b1 move stencila to preassemble 2019-07-16 08:35:35 +02:00
Min RK b6ab2a9986 check requirements.txt for local references 
allows assemble_from_subset when requirements.txt doesn't contain any local references
 2019-07-16 07:56:11 +02:00
Min RK 5cf4f786e8 add assemble_subset 
- get_assemble_files() returns list of files needed for assembly
- if buildpack.assemble_with_subset is set, only load assemble_files
  prior to running assembly scripts. Load the rest of the repo afterward

conda opts in to this, but currently I think this works
for everything *except* requirements.txt
 2019-07-16 07:55:52 +02:00
Min RK 5ef42fc2af
Merge pull request #718 from betatim/early-r 
[MRG] Install R packages before copying repo contents
 2019-07-16 07:30:16 +02:00
David R. Pugh 399b339a4a [WIP] Version bump Conda from 4.6.14 to 4.7.5 (#719) 
Version bump conda to 4.7.5

Co-authored-by: pughdr <david.pugh@kaust.edu.sa>
 2019-07-12 18:50:11 +02:00
Tim Head 09b84811ae Make sure all loops over dict items are deterministic 2019-07-12 07:23:41 +02:00
Min RK 6385097d20 comment about multiple json events per chunk 2019-07-09 16:17:56 +02:00
Tim Head 66227f85b4 Detect failure of pre-assembly in R buildpack 
If the pre-assembly step succeeds we do not re-run it after copying the
repository contents.
 2019-07-06 16:21:29 +02:00
Tim Head dd8ba8ec18 Remove print statement and unused import 2019-07-03 06:53:59 +02:00
Min RK 19e0255bb7 include full docker progress data in push events 
Most useful is probably progressDetail.progress which is the docker rendered

Example event:

```json
  "layers": {
    "25b373f5f7f1": {
      "status": "Waiting",
      "progressDetail": {},
      "id": "25b373f5f7f1"
    },
    "e9f2b5eca21e": {
      "status": "Pushing",
      "progressDetail": {
        "current": 747589632,
        "total": 758965327
      },
      "progress": "[=================================================> ]  747.6MB/759MB",
      "id": "e9f2b5eca21e"
    },
    "7753d7e0913b": {
      "status": "Pushed",
      "progressDetail": {},
      "id": "7753d7e0913b"
    },
    "ed03b06eb165": {
      "status": "Pushed",
      "progressDetail": {},
      "id": "ed03b06eb165"
    },
    "01cb88e6c1af": {
      "status": "Pushed",
      "progressDetail": {},
      "id": "01cb88e6c1af"
    },
    "adda4de99b3d": {
      "status": "Mounted from library/buildpack-deps",
      "progressDetail": {},
      "id": "adda4de99b3d"
    },
    "3a034154b7b6": {
      "status": "Mounted from library/buildpack-deps",
      "progressDetail": {},
      "id": "3a034154b7b6"
    }
```
 2019-07-02 15:05:08 +02:00
Tim Head 0eae8dc0c4 Install R packages before copying repo contents 2019-06-28 22:09:32 +02:00
Kacper Kowalik (Xarthisius) f80fb4b39b
Handle root user case more gracefully. Fixes #696 
If user_id is root, exit only from cmdline. Raise exception if r2d was
invoked as a library.
 2019-06-28 11:46:01 -05:00
Kacper Kowalik (Xarthisius) 24234d9365
Allow absolute paths in build_script_files. Fixes #673 2019-06-28 08:44:11 -05:00
Fabien Maussion 85b0d80b16
Update target_repo_dir docstring 
See https://discourse.jupyter.org/t/users-home-in-jupyterhub/1463/3
 2019-06-27 08:58:29 +01:00
Tim Head 6e93cb06a4
Merge pull request #649 from consideRatio/pipenv-support 
[MRG/REVIEW] Support Pipfile / Pipfile.lock with pipenv
 2019-06-26 07:26:35 +02:00
Erik Sundell ec7f20e1a8 Add inline comment about '\' 2019-06-25 21:21:46 +02:00
Erik Sundell 397cb939bc Correct path typo and add note about '//' 2019-06-25 19:02:17 +02:00
Erik Sundell 7dbee81af6 Syntax typo fix 2019-06-25 17:18:10 +02:00
Erik Sundell 6d508ac5e2 Autoformatting 2019-06-25 16:57:11 +02:00
Erik Sundell b4249db4ad Pin pipenv utilized to version: 2018.11.26 2019-06-25 16:39:48 +02:00
Erik Sundell 09558802d1 Formatting opinion 
The '//' will render to '/' in the Dockerfile that allows the RUN
command to continue on a new line. I initially added a '//' within a
python string on a blank line in order to format things within the
Python file to look potentially nicer, but this is of little importance
and I have now removed it again.
 2019-06-25 16:34:15 +02:00
Erik Sundell 8eae91bc67 Install pipenv in the kernel environ 2019-06-25 16:32:47 +02:00
Erik Sundell e5d2d4dd85 Make the python environment explicit during pip install 2019-06-25 16:30:02 +02:00
Tim Head 41da67490f Move more R config to the build phase 2019-06-25 13:17:56 +02:00
Tim Head 10ca25d986 Install APT packages before copying the repo contents 2019-06-25 12:57:54 +02:00
Tim Head 391f5bf4af
Revert "[MRG] Remove more files during the image build to slimdown the image" 2019-06-24 15:01:44 +02:00
Erik Sundell 61a00f7929 Improve code readability 2019-06-24 07:35:31 +02:00
Erik Sundell e5160e4b3f Autoformatting 2019-06-23 06:38:31 +02:00
Erik Sundell fe2d9b9e0d Pipfile support for Python 2 as well 2019-06-23 06:29:15 +02:00
Erik Sundell 7bb5a92ff8 Fix Pipfile buildpacks python version detection 2019-06-22 18:07:17 +02:00
Erik Sundell 2189777198 Fix Pipfile buildpack's docstring 2019-06-22 17:58:36 +02:00
Erik Sundell c9fd0a99c8 Clarify Pipfile's use of relative paths 2019-06-22 17:51:48 +02:00
Erik Sundell a8c232e6a5 Adjust copied notes to the Pipfile buildpack 2019-06-22 17:35:35 +02:00
Erik Sundell 8153fd9b4d
Fix typo 
Co-Authored-By: Tim Head <betatim@gmail.com>
 2019-06-22 16:03:44 +02:00
Tim Head 199d14a4a3
[MRG] Remove more files during the image build to slimdown the image (#709) 
[MRG] Remove more files during the image build to slimdown the image
 2019-06-22 15:17:56 +02:00
Tim Head 7019022ebf
Add support for julia 1.0.4 and 1.1.1 (#710) 
Add support for julia 1.0.4 and 1.1.1
 2019-06-22 08:01:04 +02:00
David Anthoff 923f3acbec Run black again 2019-06-21 22:38:25 +02:00
Tim Head 2ae1dde012 Switch to using -L for `find` instead of -follow 2019-06-21 21:48:02 +02:00
David Anthoff 4fa72f691b Reformat 2019-06-21 21:41:19 +02:00
Tim Head 76d6113d65 Remove more files during the image build to slimdown the image 2019-06-20 22:55:26 +02:00
Tom Morrell 93147888c5 Reformatting and better tests 2019-06-20 13:22:17 -07:00
David Anthoff 462f723b84 Add support for julia 1.0.4 and 1.1.1 2019-06-20 20:30:32 +02:00
Tom Morrell 87f33e3b6a Full generalization and support for CaltechDATA 2019-06-18 15:11:06 -07:00
Tom Morrell d2016bb722 rename 2019-06-13 12:22:31 -07:00
Tom Morrell f35e2a0382 More general doi to url 2019-06-13 11:27:24 -07:00
Tom Morrell 10fc5b5f36 Formatting 2019-06-13 11:14:16 -07:00
Tom Morrell 2db395ac87 Initial, incomplete generalization 2019-06-13 11:09:34 -07:00
Erik Sundell 6de7a8c97a Black formatting applied 2019-06-04 09:14:32 +02:00
Erik Sundell e58b5c316e Merge remote-tracking branch 'upstream/master' into pipenv-support 2019-06-04 08:53:56 +02:00
Tim Head 8b004e06dc Apply auto formatting 
Apologies to anyone finding this commit via git blame or log

run the autoformatting by

    pre-commit run --all-files
 2019-06-03 21:37:25 +02:00
Tim Head 80fbc63925
[MRG] Zenodo content provider (#693) 
[MRG] Zenodo content provider
 2019-05-30 09:47:54 +02:00
Tim Head 363c962efd Add a urlopen helper to Zenodo content provider 
Use a helper function to inject a default user-agent header into every
request we make.
 2019-05-29 22:27:09 +02:00
Tim Head e99c80799d Add comment about supporting Zenodo instances not at zenodo.org 2019-05-29 22:27:09 +02:00
Tim Head 9bda1152fb Update docstrings in Zenodo provider 2019-05-29 22:27:09 +02:00
Tim Head ec8659e62f Add tests for Zenodo content provider 2019-05-29 22:27:09 +02:00
Tim Head 2ed3818f99 Better handling of software archives 
Unpack a single ZIP file, then move it to the root of the directory
 2019-05-29 22:27:09 +02:00
Tim Head dce6c1e8d7 Add basic Zenodo content provider 2019-05-29 22:27:09 +02:00
yuvipanda b6d35b600b Upgrade JupyterHub to 1.0 2019-05-29 12:11:28 -07:00
Min RK f5d05903c6 set CONDA_DEFAULT_ENV in activate script as well 2019-05-24 11:25:56 +02:00
Min RK f5999a0b61 set CONDA_DEFAULT_ENV 
so that `conda install` commands affect the kernel environment instead of the base env

This should preserve `conda install` behavior for Dockerfiles that inherit from r2d images.
This behavior is already managed by the ENTRYPOINT which properly activates the env.
 2019-05-24 10:51:18 +02:00
Tim Head 02e0de8717 Add test that default username is picked 2019-05-23 09:45:28 +02:00
Tim Head 02ec2255d6 Use getpass instead of pwd to fetch username 
getpass is available onn windows as well as unix, whereas pwd is not
available on windows.
 2019-05-23 09:45:28 +02:00
Erik Sundell 9faeaefcf4 extract pipfile: get binder_dir right finally 
While trying to update the buildpack for changes in the PR that added
support for using a .binder directory I regressed to faulty logic. This
PR fixes that, adds some comments to avoid it, and get's things right
enough to manage to get the tests to succeed.
 2019-05-12 17:26:52 +02:00
Erik Sundell 42787d28f7 extract pipfile: add to ordered list 2019-05-12 15:57:03 +02:00
Erik Sundell 2b0aa99d84 Merge remote-tracking branch 'upstream/master' into pipenv-support 2019-05-12 15:44:10 +02:00
Erik Sundell 258271f780 extract pipfile: refine PipfileBuildPack 2019-05-12 15:36:42 +02:00
Erik Sundell 66e63f66ac extract pipfile: reset PythonBuildPack 2019-05-12 15:14:51 +02:00
Erik Sundell c25aa81c2a extract pipfile: copy PythonBuildPack 2019-05-12 15:09:14 +02:00
Kacper Kowalik (Xarthisius) caef6686d1
Do not try to build the image with root as the primary user 
Fixes #267 and #395
 2019-05-09 13:06:02 -05:00
Tim Head e66f0af23c
Revert "[MRG] Do not try to build the image with root as the primary user." 2019-05-09 13:14:32 +02:00