Bump micromamba to 1.5.8

[corneliusroemer]

Resolves #366

Mirrors #301

Description of proposed changes

Related issue(s)

Checklist

• Checks pass
• Changelog updated

[tsibley]

+1 for bumping, especially for the Zstandard support. Did you review the Micromamba release notes between 1.1.0 and 1.5.8 for breaking changes?

[tsibley]

This works locally for me now, but the very first time I ran it (after I pushed my updates), I ran into this error:

$ nextstrain setup --force conda
Setting up conda…
Removing existing directory /home/tom/.nextstrain/runtimes/conda/micromamba to start fresh…
Requesting Micromamba from https://api.anaconda.org/download/conda-forge/micromamba/1.5.8/linux-64/micromamba-1.5.8-0.tar.bz2…
Downloading and extracting Micromamba to /home/tom/.nextstrain/runtimes/conda/micromamba…
Removing existing directory /home/tom/.nextstrain/runtimes/conda/env to start fresh…
Installing Conda packages into /home/tom/.nextstrain/runtimes/conda/env…
  - nextstrain-base ==20240501T220407Z
bioconda/noarch (check zst)                         Checked  0.1s
bioconda/linux-64 (check zst)                       Checked  0.2s
nextstrain/linux-64 (check zst)                     Checked  0.2s
nextstrain/noarch                                  116.0 B @ 566.0 B/s  0.2s
conda-forge/noarch                                  14.6MB @  32.8MB/s  0.6s
conda-forge/linux-64                                34.2MB @  38.5MB/s  1.0s
bioconda/linux-64                                    5.4MB @   4.6MB/s  1.2s
bioconda/noarch                                      5.2MB @   3.9MB/s  1.2s
nextstrain/linux-64                                 25.2kB @  14.7kB/s  1.7s

Transaction

  Prefix: /home/tom/.nextstrain/runtimes/conda/env

  Updating specs:

   - nextstrain-base==20240501T220407Z


  Package                              Version  Build                  Channel          Size
──────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                          0.1  conda_forge            conda-forge       3kB
  + ca-certificates                   2024.2.2  hbcca054_0             conda-forge     155kB
  + ld_impl_linux-64                      2.40  h55db66e_0             conda-forge     713kB

[…]

  Summary:

  Install: 314 packages

  Total download: 466MB

──────────────────────────────────────────────────────────────────────────────────────────────



Transaction starting
ld_impl_linux-64                                   713.3kB @   9.9MB/s  0.1s
python_abi                                           6.4kB @  88.4kB/s  0.1s
_libgcc_mutex                                        2.6kB @  28.7kB/s  0.1s
[+] 0.1s
Downloading  (5) ╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 877.7kB / 465.9MB libstdcxx-ng               0.0s
Extracting   (4) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━       0 /     314 _libgcc_mutex              0.0sterminate called after throwing an instance of 'std::logic_error'
  what():  basic_string: construction from null is not valid
Error running ('/home/tom/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/home/tom/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20240501T220407Z', '--prefix', '/home/tom/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')
Traceback (most recent call last):
  File "/home/tom/nextstrain/cli/nextstrain/cli/runner/conda.py", line 389, in micromamba
    subprocess.run(argv, env = env, check = True)
  File "/home/tom/.pyenv/versions/3.11.4/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('/home/tom/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/home/tom/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20240501T220407Z', '--prefix', '/home/tom/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')' died with <Signals.SIGABRT: 6>.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/tom/nextstrain/cli/nextstrain/cli/runner/conda.py", line 275, in setup_prefix
    micromamba("create", install_spec)
  File "/home/tom/nextstrain/cli/nextstrain/cli/runner/conda.py", line 391, in micromamba
    raise InternalError(f"Error running {argv!r}") from err
nextstrain.cli.errors.InternalError: Error running ('/home/tom/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/home/tom/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20240501T220407Z', '--prefix', '/home/tom/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')

Set up failed!

This is an error inside micromamba. I have not been able to replicate it with either a) repeated invocations or b) downgrading back to 1.1.0 and trying the upgrade again.

[tsibley]

As part of the fixups I pushed, I also reviewed the changelog for Mamba/Micromamba and found no backwards compat issues between 1.1.0 and 1.5.8.