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146 Commits
Author SHA1 Message Date
mvdbeek da334f1e42 Fix first startup when only python3 is on PATH 2022-08-08 16:28:26 +02:00
Nicola Soranzo 2e2403e1e2 Prefer venv module over virtualenv 
if it's installed as part of the Python standard library.
 2022-06-17 00:33:14 +01:00
Dannon Baker fdcf8c086e Actually pass plugin path through to invoked build process 2022-04-04 15:15:10 -04:00
Dannon Baker 256a4495fe Pass config path to gulp 2022-04-04 10:15:55 -04:00
Dannon Baker 6240a5ab57 Slight reorg in common_startup 2022-04-04 08:55:46 -04:00
Marius van den Beek fa3ae1d6c6 Merge pull request #13358 from mvdbeek/codecoverage 
Report code coverage (for pytest test suites)
 2022-02-18 17:02:50 +01:00
Dannon Baker 29a7489590 Merge remote-tracking branch 'upstream/release_22.01' into dev 2022-02-16 14:02:31 -05:00
Nate Coraor 0297eb1bc8 Ensure $GRAVITY_STATE_DIR is present in venv activate script any time 
run.sh/common_startup.sh is called normally (without --skip-venv or
--no-create-venv).
 2022-02-16 10:09:50 -05:00
Nate Coraor 85dcd60d4c Remove node_modules when upgrading Node 2022-02-14 10:31:46 -05:00
mvdbeek 4dca001b5d Do verify certs 
You'll be running into problems later on anyway, and it doesn't look
like there are builds with known shasums anymore for more recent
virtualenv zipapps.
 2022-02-11 17:25:50 +01:00
mvdbeek d938357d8e Update virtualenv 2022-02-11 17:25:50 +01:00
Nicola Soranzo a8f5965ba6 Fix gravity requirement for Poetry 
For VCS references, need to specify the branch if it's not `master`.

Also:
- Update Poetry download link
- Require pip >= 19.3 to support direct references as requirement
  specifiers
  https://www.python.org/dev/peps/pep-0440/#direct-references
 2022-01-31 15:09:35 +00:00
Nate Coraor a53ef1888d If creating venv, modify activate to set $GRAVITY_STATE_DIR so that 
gravity can be used anywhere once the venv is activated.
 2022-01-21 09:51:34 -05:00
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
Nicola Soranzo b779aeb21a Merge branch 'release_21.05' into release_21.09 2021-12-03 12:56:28 +00:00
Nicola Soranzo 262ab8386c Increase pip minimum version in startup script 
Pip <19.0 cannot install abi3 wheels, so for example on Python >3.6 it
would (try to) build a cryptography wheel, which is not needed since
cp36-abi3 wheels are already available on PyPI:
https://cryptography.io/en/latest/faq/#why-are-there-no-wheels-for-my-python3-x-version

Fix https://github.com/galaxyproject/galaxy/issues/13023 .

xref: https://github.com/galaxyproject/planemo/issues/1208#issuecomment-984831111
 2021-12-03 11:02:20 +00:00
mvdbeek fdb36c7ed7 Run client-y tests with --frozen-lockfile 
Seems to be best-practice and may be a little faster
 2021-06-30 13:06:24 +02:00
Dannon Baker 00270ace03 Drop CLIENT_DEV_SERVER from webserver internals completely (we just proxy instead) 2021-03-05 09:52:02 -05:00
Nicola Soranzo 70def633f1 Replace pipenv with poetry. Update all dependencies 2021-01-21 20:30:00 +00:00
Nicola Soranzo 2c3f63751a Fix py27-first_startup Travis job to actually use Python 2 
`scripts/common_startup.sh` now prefers python3 when creating Galaxy's
virtual environment, so it needs to be run when inside the tox virtualenv,
where `GALAXY_PYTHON` is defined.
 2020-02-25 11:54:27 +00:00
Nicola Soranzo 437f51c2a6 Create Python3 virtualenv by default 
- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
 2020-02-09 02:54:24 +00:00
Dannon Baker fe6313ce8d If we're running webpack dev server, skip the client build on startup. 2019-11-21 17:19:54 -05:00
Dannon Baker 9d1e784868 Alternate approach to plugin building; this should be useful as a stepping stone towards moving these out of the repo completely, and it'll work *right now*. 2019-09-06 14:56:10 -04:00
Dannon 053510678f Merge pull request #8474 from bgruening/node-conda 
Node is called nodejs in conda land.
 2019-08-20 11:36:38 -04:00
Nicola Soranzo ca226282f1 Fix startup checks when using a Conda env 
Unless `--skip-venv` is specified, Galaxy creates/activates a virtualenv
also when using a Conda environment.
 2019-08-19 01:28:35 +01:00
Björn Grüning 4a2c316cfe node is called nodejs in conda-land 2019-08-17 15:42:38 +02:00
Dannon Baker 877bd322d6 Add pointer to client/README.md to address 'https://github.com/galaxyproject/galaxy/commit/8bb2b6bfbcac89910ec6b5cc58e23243571ab879#commitcomment-34259049' 2019-08-14 09:59:55 -04:00
Nicola Soranzo e7165c37e3 Fix issues reported by shellcheck 2019-07-17 12:46:46 +01:00
Nicola Soranzo 8e8c64308a Fix use of `PIP_PROGRESS_BAR` env variable 
`PIP_PROGRESS_BAR` environment variable is used by `pip` to set the value
for the `--progress-bar` option. It seems that specifying it also only the
command line does not override it in some configurations, e.g. on TravisCI
Linux builds of BioBlend, see e.g.

https://travis-ci.org/galaxyproject/bioblend/jobs/558857557
 2019-07-16 17:17:32 +01:00
Marius van den Beek 64c71ca7e1 Merge pull request #8290 from natefoo/remove-ci-pip-progress-bar 
Don't show the pip progress bar when installing under CI
 2019-07-09 12:17:49 +02:00
Nate Coraor 118e01f796 Don't show the pip progress bar when installing under CI 2019-07-07 14:22:07 +02:00
Nate Coraor 37522f5e8e Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-05 16:05:17 +02:00
Nate Coraor cdb9040e26 Merge remote-tracking branch 'origin/dev' into installable 2019-07-05 15:51:15 +02:00
Nicola Soranzo 1b1f6e9cda Fix comments 2019-04-14 18:02:42 +01:00
Dannon Baker 485eece7f3 Grammatical tweaks. 2019-03-26 09:31:33 -04:00
Dannon Baker 8bb2b6bfbc Add extra verbosity covering non-client-building branches in startup. 2019-03-26 09:04:45 -04:00
Martin Cech e65604bc06 Merge pull request #7556 from jmchilton/expression_tools 
Implement expression tools and non-data tool outputs.
 2019-03-20 18:52:59 -04:00
mvdbeek 5e778f4812 Install node as part of common_startup.sh 2019-03-20 10:02:56 +01:00
Dannon Baker 99082ff486 Drop plugin staging from common_startup 2019-03-14 11:40:52 -04:00
Hervé Ménager 557407c384 correct virtualenv download with no wget/curl 
the embedded python code needs a small correction to work in the no curl/wget available case.
 2019-03-06 16:24:07 +01:00
Nate Coraor ef8f208002 Merge remote-tracking branch 'upstream/release_19.01' into dev 2019-02-22 13:24:15 -05:00
Dannon Baker 726ad9a0f6 Bump yarn's network timeout from 2 minutes to 5 minutes. 2019-02-21 11:48:11 -05:00
Nicola Soranzo c6f1183939 Update documentation about dependencies 2019-02-18 22:36:32 +00:00
Sergey Golitsynskiy c21e07e1a0 Do not default to DEV_WHEELS=1 if no Git is found 
If there is no Git repo in a Galaxy install, DEV_WHEELS will not be
turned on by default. If they are needed, use the --dev-wheels flag.

(Current behavior: common_startup.sh will turn on the DEV_WHEELS option
if no git repo is found, making the assumption that it is dealing with a
dev install. Thus, dev dependencies are installed whenever there's no
Git repo, including the use case when Galaxy was downloaded as a tarball
- when they may or may not be desired. There is no option to override
this behavior without editing the script.)
 2019-02-15 17:05:48 -05:00
Dannon Baker 4427d3a982 Separate client node version requirement into individual dotfile for easier reading/use in ansible playbooks 2019-02-13 14:52:08 -05:00
Nicola Soranzo 21ce99e231 Merge branch 'release_19.01' into dev 2019-02-12 12:03:03 +00:00
Nicola Soranzo b33b06440f Merge branch 'release_18.09' into release_19.01 2019-02-12 11:51:07 +00:00
Dannon Baker a10d2c51d3 Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) 2019-01-18 11:54:59 -05:00
Dannon Baker bad8cffdbc Verify .venv's node version is in line with what we've specified as being locked, rather than just checking if node exists. 2019-01-15 14:24:12 -05:00
Nicola Soranzo 975c8b605f Fix activation of `_galaxy_` conda env 
- Use `conda_activate`, which works also under dash
- Run `conda_activate` also when `$GALAXY_CONDA_ENV` already exists
- Run `virtualenv` when the conda env is active but `$GALAXY_VIRTUAL_ENV`
  does not exist
- Update the default for `GALAXY_CONDA_ENV` in
  scripts/common_startup_functions.sh

Follow-up on https://github.com/galaxyproject/galaxy/pull/6975 .
 2018-12-14 00:22:12 +00:00