Update upper bound for galaxy packages to < 23.2

[bernt-matthias]

... waiting for the 23.1 release :)

[bernt-matthias]

Test is failing reproducibly. But not sure if related.

[bgruening]

The error I can see is:

E           PackagesNotFoundError: The following packages are not available from current channels:
E           
E             - fleeqtk
E           
E           Current channels:
E           
E             - https://conda.anaconda.org/conda-forge/linux-64
E             - https://conda.anaconda.org/conda-forge/noarch
E             - https://conda.anaconda.org/bioconda/linux-64
E             - https://conda.anaconda.org/bioconda/noarch
E             - https://repo.anaconda.com/pkgs/main/linux-64
E             - https://repo.anaconda.com/pkgs/main/noarch
E             - https://repo.anaconda.com/pkgs/r/linux-64
E             - https://repo.anaconda.com/pkgs/r/noarch

Which is true. This packages does not exist, its a fake package that is build locally during a test.

I think --conda_use_local is not working in this PR.

[bernt-matthias]

Tried to execute the commands manually and got

/tmp/tmpn84st44m/miniconda3/bin/conda build /home/berntm/projects/planemo/project_templates/conda_answers/exercise_2/fleeqtk   

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/tmp/tmpn84st44m/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1132, in __call__
        return func(*args, **kwargs)
      File "/tmp/tmpn84st44m/miniconda3/lib/python3.10/site-packages/conda/cli/main.py", line 69, in main_subshell
        exit_code = do_call(args, p)
      File "/tmp/tmpn84st44m/miniconda3/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 115, in do_call
        return args.plugin_subcommand.action(sys.argv[2:])
      File "/tmp/tmpn84st44m/miniconda3/lib/python3.10/site-packages/conda_build/plugin.py", line 10, in build
        execute(*args, **kwargs)
      File "/tmp/tmpn84st44m/miniconda3/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 516, in execute
        _parser, args = parse_args(args)
      File "/tmp/tmpn84st44m/miniconda3/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 470, in parse_args
        check_recipe(args.recipe)
    AttributeError: 'Namespace' object has no attribute 'recipe'

`$ /tmp/tmpn84st44m/miniconda3/bin/conda build /home/berntm/projects/planemo/project_templates/conda_answers/exercise_2/fleeqtk`

  environment variables:
                 CIO_TEST=<not set>
    CONDA_ALLOW_SOFTLINKS=false
                CONDA_EXE=/home/berntm/miniconda3/bin/conda
         CONDA_PYTHON_EXE=/home/berntm/miniconda3/bin/python
               CONDA_ROOT=/tmp/tmpn84st44m/miniconda3
              CONDA_SHLVL=0
           CURL_CA_BUNDLE=<not set>
            DEFAULTS_PATH=/usr/share/gconf/gnome-xorg.default.path
               LD_PRELOAD=<not set>
           MANDATORY_PATH=/usr/share/gconf/gnome-xorg.mandatory.path
                     PATH=/tmp/venv-planemo/bin:/usr/local/go/bin:/home/berntm/perl5/bin:no:/hom
                          e/berntm/bin:/home/berntm/.local/bin:/home/berntm/miniconda3/condabin:
                          /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/game
                          s:/usr/local/games:/snap/bin:/snap/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
               WINDOWPATH=2

     active environment : None
            shell level : 0
       user config file : /home/berntm/.condarc
 populated config files : /tmp/tmpn84st44m/miniconda3/.condarc
                          /home/berntm/.condarc
          conda version : 23.3.1
    conda-build version : 3.27.0
         python version : 3.10.12.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /tmp/tmpn84st44m/miniconda3  (writable)
      conda av data dir : /tmp/tmpn84st44m/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/anaconda/linux-64
                          https://conda.anaconda.org/anaconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /tmp/tmpn84st44m/miniconda3/pkgs
                          /home/berntm/.conda/pkgs
       envs directories : /tmp/tmpn84st44m/miniconda3/envs
                          /home/berntm/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.31.0 CPython/3.10.12 Linux/5.15.0-83-generic ubuntu/22.04.3 glibc/2.35
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]: ^C
Timeout reached. No report sent.

Might be solved by an update to conda conda/conda-build#4984 (comment)

[bernt-matthias]

Bumping conda helps with the failing test. Let's see if there are side effects galaxyproject/galaxy#17013

[nsoranzo]

I am not sure how galaxyproject/galaxy#17013 can help, it bumps the minimum conda version but in tests it's most likely that the latest conda version is installed either way.

[bernt-matthias]

All I know is that in the failing test on my local computer not the latest was installed, but:

           conda version : 23.3.1
    conda-build version : 3.27.0

When I bumped the minimum requirement the tests were successful. No idea how to test this here, without bumping the Galaxy packages first. Can we somehow patch tool-util during the test?

[nsoranzo]

All I know is that in the failing test on my local computer not the latest was installed, but:

           conda version : 23.3.1
    conda-build version : 3.27.0

Is that what you have in ~/miniconda3 ?

When I bumped the minimum requirement the tests were successful. No idea how to test this here, without bumping the Galaxy packages first. Can we somehow patch tool-util during the test?

Did you update the conda package manually? Changing CONDA_PACKAGE_SPECS only affects new conda installations.

[nsoranzo]

What's weird when looking at the CI logs is that test_local_conda_dependencies_version failed at the planemo test stage, when the [email protected] conda environment should have been created already by planemo conda_install right before.

[bernt-matthias]

What's weird when looking at the CI logs is..

Yes. They had exit code 0, despite the failure.

[mvdbeek]

Can you check in the github workflow if there is any interference from the conda or .condarc already installed on the VM ?

[bernt-matthias]

So, now we see the error from the build step. Seems that this installs 23.3.1 .. my hypothesis is as follows:

• the mambaforge installer comes with preinstalled conda 23.3.1 (just verified)
• when installing conda use the two-step approach
  1. try to fulfill requirements such that installed packages don't need to be updated
  2. if this is not possible fulfill requirements and allow updating installed packages

so with our current conda pins, we are stuck at 23.3.1 (maybe also because we install in the base env?) and not the newest packages are installed.

Does this sound reasonable?

Note that also planemo conda_search seems not to use the exit code of the exec_command function. If desired I could try to fix it here.

[nsoranzo]

Thanks @bernt-matthias , the latest commit to check the exit code really helped clarifying the issue, and your explanation makes sense. I didn't expect the latest Mambaforge to install conda 23.3.1, but any way it looks like that galaxyproject/galaxy#17013 is the correct solution here.

Note that also planemo conda_search seems not to use the exit code of the exec_command function. If desired I could try to fix it here.

Yes, that would be good, thanks!

[nsoranzo]

planemo/commands/cmd_conda_install.py also has the same issue.

[bernt-matthias]

Does anyone have an idea what's going on with the 3.7 tests?

[mvdbeek]

dev doesn't work on 3.7, that's why I rebased your PR

[mvdbeek]

Very cool, thanks @bernt-matthias