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162 Commits
Author SHA1 Message Date
Nicola Soranzo 0a73e1c512 Merge branch 'release_23.0' into release_23.1 2023-07-24 15:16:11 +01:00
Nicola Soranzo c7db0bbeca Do not install npm/yarn via conda if they already available at the correct version 2023-07-21 00:58:36 +01:00
Nicola Soranzo a9b2a4f7b0 Code refactoring 
Simplification allowed by commit 39c0000c1b .
 2023-07-21 00:58:36 +01:00
Matthias Bernt 1b2ac2a212 also set galaxy config file variable in common startup 
otherwise GALAXY_CONDITIONAL_DEPENDENCIES can not be determined.
in run.sh set_galaxy_config_file_var is called only after common_startup
is called.
 2023-07-21 00:58:35 +01:00
Matthias Bernt bb90e3b5dc activate the conda env before the python venv 
and install node and yarn via conda if a conda env is used
 2023-07-21 00:58:35 +01:00
Nicola Soranzo 387aa1dd48 Test first startup on macOS also with Python 3.11 
- Allow passing GALAXY_CONDA_PYTHON_VERSION environment variable to
  the startup script to specify the Python version to use when
  creating the `_galaxy_` conda environment.
- Some Shellcheck fixes.
 2023-07-21 00:58:33 +01:00
Matthias Bernt 92806a97a5 Improve log message wording 2023-07-20 18:32:00 +01:00
Nicola Soranzo 36ed2d5ae2 Merge branch 'release_23.0' into release_23.1 2023-07-13 10:25:48 +01:00
Nicola Soranzo 62497462e0 Don't always install node in the virtualenv 
if it's already installed system-wide at the correct version.

Prevent node installation issues during CI builds where we install
node with the setup-node action but it was ignored because it was
not inside the virtualenv, e.g.:

https://github.com/galaxyproject/galaxy/actions/runs/5530959878/jobs/10091018774
 2023-07-12 19:26:02 +01:00
Nicola Soranzo 940ff9fe36 Test first startup on macOS also with Python 3.11 
- Allow passing GALAXY_CONDA_PYTHON_VERSION environment variable to
  the startup script to specify the Python version to use when
  creating the `_galaxy_` conda environment.
- Some Shellcheck fixes.
 2023-05-12 15:45:39 +01:00
John Davis e08e1aaa9f Drop tool shed bootstrapping scripts and references to them 2023-02-08 00:33:48 -05:00
John Chilton 235ef39f16 deployment testing 2023-01-26 13:45:42 -05:00
Dannon Baker 9b6dd967c2 Basic client installation command added 2023-01-20 10:19:48 -05:00
Nicola Soranzo 39c0000c1b Bump minimum pip version to 20.3 . Ignore `--replace-pip and --no-replace-pip` startup options 
Pip 20.3 added support for PEP 600, i.e. manylinux wheels using platform
tags of the form "manylinux_${GLIBCMAJOR}_${GLIBCMINOR}_${ARCH}". Fix
installation of dependencies like pysam 0.20.0 wheels, which otherwise need
to be built from source and can fail as reported by @assuntad23 in
https://gist.github.com/assuntad23/3022db63a6878f044a209961dd40e592

Also:
- Install `wheel` to fix warning like `Using legacy setup.py install for
  beaker, since package 'wheel' is not installed.`
- Drop unnecessary `defaults` channel from conda commands.
- Fix "SC2223: This default assignment may cause DoS due to globbing. Quote
  it." errors reported by `shellcheck -x` .
 2023-01-17 15:01:38 +00:00
Nate Coraor 1684da5c15 Don't modify venv activate to set $GRAVITY_STATE_DIR 2022-12-05 12:52:11 -05:00
Nicola Soranzo 0df5c9a5fb Updates for Poetry 1.2.0 
Also:
- Export only dev requirements to `lib/galaxy/dependencies/dev-requirements.txt` .
- Packages don't have a `requirements.txt` file.
 2022-09-05 17:23:18 +01:00
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