Remove defaults channel

[leehart]

No description provided.

[leehart]

Currently raisingEnvironmentLocationNotFound 🤔

[mgenv] installing packages
[mgenv] install conda
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/runner/work/mgenv/mgenv/deps/conda

  added / updated specs:
    - conda-libmamba-solver


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    ca-certificates-2024.8.30  |       hbcca054_0         155 KB  conda-forge
    certifi-2024.8.30          |     pyhd8ed1ab_0         160 KB  conda-forge
    conda-24.9.2               |  py312h7900ff3_0         1.1 MB  conda-forge
    conda-libmamba-solver-24.9.0|     pyhd8ed1ab_0          41 KB  conda-forge
    libexpat-2.6.2             |       h59595ed_0          72 KB  conda-forge
    libgcc-14.2.0              |       h77fa898_1         829 KB  conda-forge
    libgcc-ng-14.2.0           |       h69a702a_1          53 KB  conda-forge
    libgomp-14.2.0             |       h77fa898_1         450 KB  conda-forge
    libnsl-2.0.1               |       hd590300_0          33 KB  conda-forge
    libsqlite-3.46.0           |       hde9e2c9_0         845 KB  conda-forge
    libuuid-2.38.1             |       h0b41bf4_0          33 KB  conda-forge
    libxcrypt-4.4.36           |       hd590300_1          98 KB  conda-forge
    libzlib-1.2.13             |       h4ab18f5_6          60 KB  conda-forge
    openssl-3.3.2              |       hb9d3cd8_0         2.8 MB  conda-forge
    python-3.12.2              |hab00c5b_0_cpython        30.8 MB  conda-forge
    python_abi-3.12            |          5_cp312           6 KB  conda-forge
    zlib-1.2.13                |       h4ab18f5_6          91 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        37.6 MB

The following NEW packages will be INSTALLED:

  libexpat           conda-forge/linux-64::libexpat-2.6.2-h59595ed_0 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6 
  python_abi         conda-forge/linux-64::python_abi-3.12-5_cp312 

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2024.7.2-h~ --> conda-forge::ca-certificates-2024.8.30-hbcca054_0 
  certifi            pkgs/main/linux-64::certifi-2024.7.4-~ --> conda-forge/noarch::certifi-2024.8.30-pyhd8ed1ab_0 
  conda              pkgs/main::conda-24.7.1-py312h06a4308~ --> conda-forge::conda-24.9.2-py312h7900ff3_0 
  conda-libmamba-so~ pkgs/main::conda-libmamba-solver-24.7~ --> conda-forge::conda-libmamba-solver-24.9.0-pyhd8ed1ab_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-14.2.0-h69a702a_1 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-14.2.0-h77fa898_1 
  libuuid              pkgs/main::libuuid-1.41.5-h5eee18b_0 --> conda-forge::libuuid-2.38.1-h0b41bf4_0 
  openssl              pkgs/main::openssl-3.0.14-h5eee18b_0 --> conda-forge::openssl-3.3.2-hb9d3cd8_0 
  zlib                    pkgs/main::zlib-1.2.13-h5eee18b_1 --> conda-forge::zlib-1.2.13-h4ab18f5_6 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 
  python                pkgs/main::python-3.12.4-h5148396_1 --> conda-forge::python-3.12.2-hab00c5b_0_cpython 



Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Python 3.12.2
conda 24.9.2
# packages in environment at /home/runner/work/mgenv/mgenv/deps/conda:
#
# Name                    Version                   Build  Channel

conda-libmamba-solver     24.9.0             pyhd8ed1ab_0    conda-forge
EnvironmentLocationNotFound: Not a conda environment: /home/runner/work/mgenv/mgenv/deps/conda/envs/mgenv-5aba65e

Error: Process completed with exit code 1.

[ahernank]

@leehart haven't had a chance to properly think about this one, but just saw in https://github.com/wtsi-hgi/conda-audited that they add the nodefaults channel instead, might be an alternative? Seems to be equivalent to --override-channels.

[leehart]

Thanks @ahernank . Judging from https://stackoverflow.com/questions/67695893/how-do-i-completely-purge-and-disable-the-default-channel-in-anaconda-and-switch
it looks like nodefaults might only be applicable to the channels list in the YAML, but here we're creating the YAML files using conda create, so the --override-channels arg seems appropriate. I haven't tried it yet though!

In this context, I suppose we could try something like:

CHANNEL_OPTS="--channel conda-forge --channel bioconda --channel nodefaults"

Judging from the docs https://docs.conda.io/projects/conda/en/4.6.1/user-guide/tasks/manage-environments.html I would expect it to either raise an error (e.g. "channel nodefaults not found") or result in the same behaviour as using --override-channels without defaults, which would seem to be the conventional approach. I'll see what happens, but it would feel a bit hacky and unsatisfactory if it works!

I suspect there might be a simple reason for EnvironmentLocationNotFound being raised here, when we just take out the defaults channel, but I'm still a bit puzzled.

[leehart]

Tests via #154 seem to suggest some other cause of EnvironmentLocationNotFound that is unrelated to the removal of the defaults channel, and also convinces me that nodefaults wouldn't be applicable here.

I suspect that just removing the defaults channel in the conventional way will work once we debug the EnvironmentLocationNotFound error.

[leehart]

I'm tempted to try just a standard update of the malariagen_data package in a new PR, while removing the defaults channel, because this process usually works when we are making that sort of change.

[leehart]

EnvironmentLocationNotFound happens in the context of package upgrade too, PR #156

I suppose it's either one of the changes in the PR or something different about the CI environment, e.g. the resources being pulled down by install-conda.sh. It was evidently working at the end of September, i.e. PR #150

[leehart]

I've confirmed that simply removing the pinned files and attempting to upgrade a package (as usual, without changing any channels) results in the same error, which I've logged as issue #158.