nextstrain update conda fails silently

[joverlee521]

Running the standalone version of 7.1.0 I get:

$ nextstrain update conda
Checking for newer versions of Nextstrain CLI…

nextstrain-cli is up to date!

Updating conda runtime…
Updating Conda package nextstrain-base from 20230615T171309Z to 20230717T174555Z…

Updating Conda packages in /Users/jlee2346/.nextstrain/runtimes/conda/env…
  - nextstrain-base ==20230717T174555Z

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

nextstrain/noarch                                  130.0 B @ 414.0 B/s  0.3s
nextstrain/osx-64                                   30.2kB @  72.7kB/s  0.4s
bioconda/osx-64                                      4.2MB @   3.9MB/s  1.2s
bioconda/noarch                                      4.6MB @   3.3MB/s  1.3s
conda-forge/noarch                                  13.4MB @   4.3MB/s  3.7s
conda-forge/osx-64                                  29.8MB @   4.1MB/s  8.6s
Transaction

  Prefix: /Users/jlee2346/.nextstrain/runtimes/conda/env

  All requested packages already installed


Transaction starting
Transaction finished
Cleaning up…

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

Collect information..
Cleaning index cache..
Cleaning lock files..
Cleaning tarballs..
Cleaning packages..

Runtime updated!

Then when i check the version output again, it's still using the old nextstrain-base:

$ nextstrain version --verbose
nextstrain.cli 7.1.0

Python
  /Users/jlee2346/.nextstrain/cli-standalone/nextstrain
  3.10.9 (main, Dec 21 2022, 05:06:54) [Clang 14.0.3 ]

Runners
  docker (default)
    nextstrain/base:latest (18b46ee75a34, 2023-07-19 18:20:45 -0700 PDT)
    augur 22.1.0
    auspice v2.46.1
    fauna 59dfaec
    sacra not present

  conda 
    nextstrain-base 20230615T171309Z (h0dc7051_0_locked, nextstrain/label/main)
    augur 22.0.3
    auspice 2.46.0

  singularity 
    docker://nextstrain/base (not present)

  ambient 
    auspice 2.46.0

  aws-batch 
    unknown

[joverlee521]

This also fails to update when I try to install specific versions with the NEXTSTRAIN_* envvars:

$ NEXTSTRAIN_CONDA_CHANNEL=nextstrain/label/main \
NEXTSTRAIN_CONDA_BASE_PACKAGE="nextstrain-base ==20230628T211222Z" \
  nextstrain update conda
Checking for newer versions of Nextstrain CLI…

nextstrain-cli is up to date!

Updating conda runtime…
Updating nextstrain-base from 20230615T171309Z to ==20230628T211222Z…

Updating Conda packages in /Users/jlee2346/.nextstrain/runtimes/conda/env…
  - nextstrain-base ==20230628T211222Z

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

nextstrain/label/main/noarch                       130.0 B @ 231.0 B/s  0.6s
nextstrain/label/main/osx-64                        30.2kB @  34.1kB/s  0.9s
bioconda/osx-64                                      4.2MB @   1.5MB/s  3.1s
bioconda/noarch                                      4.6MB @   1.1MB/s  4.0s
conda-forge/noarch                                  13.4MB @   1.7MB/s  8.8s
conda-forge/osx-64                                  29.8MB @   2.7MB/s 13.0s
Transaction

  Prefix: /Users/jlee2346/.nextstrain/runtimes/conda/env

  All requested packages already installed


Transaction starting
Transaction finished
Cleaning up…

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

Collect information..
Cleaning index cache..
Cleaning lock files..
Cleaning tarballs..
Cleaning packages..

Runtime updated!

[joverlee521]

Running the forced setup with NEXTSTRAIN_* envvars produces an actual error:

$ NEXTSTRAIN_CONDA_CHANNEL=nextstrain/label/main \
NEXTSTRAIN_CONDA_BASE_PACKAGE="nextstrain-base ==20230628T211222Z" \
  nextstrain setup --force conda
Setting up conda…
Removing existing directory /Users/jlee2346/.nextstrain/runtimes/conda/micromamba to start fresh…
Requesting Micromamba from https://api.anaconda.org/download/conda-forge/micromamba/1.0.0/osx-64/micromamba-1.0.0-1.tar.bz2…
Downloading and extracting Micromamba to /Users/jlee2346/.nextstrain/runtimes/conda/micromamba…
Removing existing directory /Users/jlee2346/.nextstrain/runtimes/conda/env to start fresh…
Installing Conda packages into /Users/jlee2346/.nextstrain/runtimes/conda/env…
  - nextstrain-base ==20230628T211222Z

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

nextstrain/label/main/osx-64                        30.2kB @  79.6kB/s  0.4s
nextstrain/label/main/noarch                       135.0 B @ 278.0 B/s  0.5s
bioconda/osx-64                                      4.2MB @   2.1MB/s  2.2s
bioconda/noarch                                      4.6MB @   1.5MB/s  3.1s
conda-forge/noarch                                  13.4MB @   2.4MB/s  6.3s
conda-forge/osx-64                                  29.8MB @   3.0MB/s 11.6s
Encountered problems while solving:
  - package nextstrain-base-20230628T211222Z-h0dc7051_0_locked requires git ==2.41.0 pl5321h5c607e1_0, but none of the providers can be installed

The environment can't be solved, aborting the operation
error    libmamba Could not solve for environment specs
critical libmamba UnsatisfiableError
Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20230628T211222Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain/label/main', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')
Traceback (most recent call last):
  File "nextstrain.cli.runner.conda", line 347, in micromamba
    subprocess.run(argv, env = env, check = True)
  File "subprocess", line 526, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20230628T211222Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain/label/main', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')' returned non-zero exit status 1.

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

Traceback (most recent call last):
  File "nextstrain.cli.runner.conda", line 233, in setup_prefix
    micromamba("create", *packages)
  File "nextstrain.cli.runner.conda", line 349, in micromamba
    raise InternalError(f"Error running {argv!r}") from err
nextstrain.cli.errors.InternalError: Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20230628T211222Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain/label/main', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')

Set up failed!

[joverlee521]

Tracked the underlying issue in nextstrain/conda-base#38, but there should still be better messages from the CLI if the runtime was not actually updated.

[joverlee521]

Ah, this could be as simple as updating the version of micromamba we are using for our conda runtime.

I overrode the default version with NEXTSTRAIN_CONDA_MICROMAMBA_VERSION=1.1.0 nextstrain setup conda --force and now it produces the expected error:

$ nextstrain update conda
Checking for newer versions of Nextstrain CLI…

nextstrain-cli is up to date!

Updating conda runtime…
Updating Conda package nextstrain-base from 20230615T171309Z to 20230717T174555Z…

Updating Conda packages in /Users/jlee2346/.nextstrain/runtimes/conda/env…
  - nextstrain-base ==20230717T174555Z

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/osx-64                                          Using cache
conda-forge/noarch                                          Using cache
bioconda/osx-64                                             Using cache
bioconda/noarch                                             Using cache
nextstrain/noarch                                             No change
nextstrain/osx-64                                             No change
error    libmamba Could not solve for environment specs
    Encountered problems while solving:
      - package nextstrain-base-20230717T174555Z-h0dc7051_0_locked requires nodejs ==18.16.1 h46e3395_0, but none of the providers can be installed
    
    The environment can't be solved, aborting the operation
    
critical libmamba Could not solve for environment specs
Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'update', 'nextstrain-base ==20230717T174555Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin')
Traceback (most recent call last):
  File "/Users/jlee2346/Repos/nextstrain/cli/nextstrain/cli/runner/conda.py", line 347, in micromamba
    subprocess.run(argv, env = env, check = True)
  File "/Users/jlee2346/.pyenv/versions/3.6.5/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'update', 'nextstrain-base ==20230717T174555Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin')' returned non-zero exit status 1.

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

Traceback (most recent call last):
  File "/Users/jlee2346/Repos/nextstrain/cli/nextstrain/cli/runner/conda.py", line 486, in update
    micromamba("update", update_spec)
  File "/Users/jlee2346/Repos/nextstrain/cli/nextstrain/cli/runner/conda.py", line 349, in micromamba
    raise InternalError(f"Error running {argv!r}") from err
nextstrain.cli.errors.InternalError: Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'update', 'nextstrain-base ==20230717T174555Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin')

Updating failed!