- 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.
- 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.
Should help with nodeenv failing in CI tests, e.g.
```
Installing node into /home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage with nodeenv.
* Install prebuilt node (18.12.1) .Incomplete read while readingfrom https://nodejs.org/download/release/v18.12.1/node-v18.12.1-linux-x64.tar.gz
.
Traceback (most recent call last):
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/bin/nodeenv", line 10, in <module>
sys.exit(main())
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 1104, in main
create_environment(env_dir, args)
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 980, in create_environment
install_node(env_dir, src_dir, args)
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 739, in install_node
install_node_wrapped(env_dir, src_dir, args)
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 762, in install_node_wrapped
download_node_src(node_url, src_dir, args)
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 602, in download_node_src
with ctx as archive:
File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 573, in tarfile_open
tf = tarfile.open(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/tarfile.py", line 1573, in open
saved_pos = fileobj.tell()
AttributeError: 'bytes' object has no attribute 'tell'
```
from https://github.com/galaxyproject/galaxy/actions/runs/4883207488/jobs/8714237674?pr=16036
- Update Python dependencies that didn't have a cp311 wheel: h5py and
psycopg2-binary.
- For packages for which there is no recent version that works on all
Python versions supported by Galaxy (numpy and scipy), replace old
requirement with multiple Python-version-specific requirements.
mvdbeek