python 3.9 tests are now failing, with error attributed to gxx conda package deactivate script

[ctb]

see e.g. #1776

fails with the same error seen over in #1772 (comment) - looks like a problem with the gxx package.

/tmp/tmpqhbgda3w: 5: /usr/share/miniconda3/envs/sourmash_dev/etc/conda/deactivate.d/deactivate-gxx_linux-64.sh: Syntax error: "(" unexpected

[ctb]

tried to recreate in various ways - I can at least get the right package with

conda install gxx_linux-64

but the precise mixture that results to the errors in that build log continue to elude me.

[ctb]

revisited today. The problem seems to occur only in the mamba job in the dev_envs.yml action see file. This job does the following, by my understanding:

• runs mamba to installpython=3.9 tox-conda rust git compilers pandoc
• runs tox -e py39

which produces the following error message when I run it on farm (after deleting .tox/py39 to ensure clean install) -

.package create: /home/ctbrown/sourmash/.tox/.package
.package installdeps: setuptools >= 48, setuptools_scm[toml] >= 4, <6, setuptools_scm_git_archive, milksnake, wheel >= 0.29.0
ERROR: invocation failed (exit code 2), logfile: /home/ctbrown/sourmash/.tox/.package/log/.package-1.log
================================== log start ===================================
/tmp/tmp98st02cc: 146: /home/ctbrown/miniconda3/envs/smash-actions2/etc/conda/deactivate.d/deactivate-gcc_linux-64.sh: Syntax error: "(" unexpected (expecting "fi")

=================================== log end ====================================
ERROR: could not install deps [setuptools >= 48, setuptools_scm[toml] >= 4, <6, setuptools_scm_git_archive, milksnake, wheel >= 0.29.0]; v = InvocationError("/home/ctbrown/sourmash/.tox/.package/bin/python -m pip install 'setuptools >= 48' 'setuptools_scm[toml] >= 4, <6' setuptools_scm_git_archive milksnake 'wheel >= 0.29.0'", 2)
py39 create: /home/ctbrown/sourmash/.tox/py39
py39 installdeps: pip >= 19.3.1
ERROR: invocation failed (exit code 2), logfile: /home/ctbrown/sourmash/.tox/py39/log/py39-1.log
================================== log start ===================================
/tmp/tmpwnuhhzhm: 146: /home/ctbrown/miniconda3/envs/smash-actions2/etc/conda/deactivate.d/deactivate-gcc_linux-64.sh: Syntax error: "(" unexpected (expecting "fi")

=================================== log end ====================================
ERROR: could not install deps [pip >= 19.3.1]; v = InvocationError("/home/ctbrown/sourmash/.tox/py39/bin/python -m pip install 'pip >= 19.3.1'", 2)
___________________________________ summary ____________________________________
ERROR:   py39: could not install deps [pip >= 19.3.1]; v = InvocationError("/home/ctbrown/sourmash/.tox/py39/bin/python -m pip install 'pip >= 19.3.1'", 2)

Note the gxx linux packages are as follows, based on mamba list --explicit | grep gxx.

https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-9.4.0-h03d3576_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gxx-9.4.0-h192d537_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gxx_linux-64-9.4.0-h0316aca_3.tar.bz2

I cannot replicate the problem by running the pip install outside of tox:

pip install 'setuptools >= 48' 'setuptools_scm[toml] >= 4, <6' setuptools_scm_git_archive milksnake 'wheel >= 0.29.0'

and oddly enough, this also works:

.tox/py39/bin/python -m pip install 'setuptools >= 48' 'setuptools_scm[toml] >= 4, <6' setuptools_scm_git_archive milksnake 'wheel >= 0.29.0'

which makes me wonder if there's something special going on with tox and conda here. ❓ ❗ ❓ ❗

[ctb]

ok, and interesting to note that tox -e py39 works just fine over in the python tests (in python.yml). The difference there may be that those tests do not use a conda environment.

(As noted, I can reproduce things on the command line, so it's not a github actions thing either.)

[ctb]

Now reproduced using a (fairly simple? :) isolated git repo - see https://github.com/ctb/2021-conda-tox-wat

[ctb]

pursuing over in conda-forge: conda-forge/ctng-compiler-activation-feedstock#60

[ctb]

it looks like this was fixed and our github actions are now working! 🎉