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.)
- 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 .
which bundles `wheel` 0.32.2.
The old virtualenv 13.1.2 included wheel 0.24.0, where tagging is broken
for Python >=3.5, producing tracebacks like:
```
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-c53eutpg/uwsgi/setup.py", line 138, in <module>
'Programming Language :: Python :: 3.6',
File "/tmp/wheel_venv/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 213, in run
archive_basename = self.get_archive_basename()
File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 161, in get_archive_basename
impl_tag, abi_tag, plat_tag = self.get_tag()
File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 155, in get_tag
assert tag == supported_tags[0]
AssertionError
```
This was fixed in wheel 0.25.0. Reported by @wm75.
Also update `urlretrieve` import for Python 3.
`logging.exception()` already adds the the exception information after
the supplied message.
Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.
xref. https://github.com/galaxyproject/galaxy/issues/1715
when `VERSION_MINOR` in `lib/galaxy/version.py` is e.g. `rc1`.
Also:
- Do not require awk
- Remove unused functions
- Do not require the presence of `~/.github.json` file
Hervé Ménager