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The Fast Cross-Platform Package Manager
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`micromamba env` does not show any environments in v2.0.2, despite having lots of environments #3500

Open corneliusroemer opened 2 days ago

corneliusroemer commented 2 days ago

Troubleshooting docs

Anaconda default channels

How did you install Mamba?

Mambaforge or latest Miniforge

Search tried in issue tracker

micromamba env

Latest version of Mamba

Tried in Conda?

I do not have this problem with Conda, just with Mamba

Describe your issue

micromamba env does not show any environments, but I definitely have many present on my system.

~ via šŸ v3.11.9 in ā˜ø aws (main) on ā˜ļø  (us-east-1)
āÆ micromamba env

I just installed v2.0.2, I don't think I had this issue with v1.5.10

I definitely do have environments, I can activate them as well:

āÆ micromamba activate py12

~ via šŸ v3.12.6 in ā˜ø aws (main) via šŸ…’ py12 on ā˜ļø  (us-east-1)
āÆ

mamba info / micromamba info

āÆ micromamba info

       libmamba version : 2.0.2
     micromamba version : 2.0.2
           curl version : libcurl/8.9.1 (OpenSSL/3.3.2) SecureTransport zlib/1.3.1 zstd/1.5.6 libssh2/1.11.0 nghttp2/1.58.0
     libarchive version : libarchive 3.7.4 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.6
       envs directories : /Users/corneliusromer/micromamba/envs
          package cache : /Users/corneliusromer/micromamba/pkgs
                          /Users/corneliusromer/.mamba/pkgs
            environment : /opt/homebrew/Caskroom/miniforge/base (active)
           env location : /opt/homebrew/Caskroom/miniforge/base
      user config files : /Users/corneliusromer/.mambarc
 populated config files : /opt/homebrew/Caskroom/miniforge/base/.condarc
                          /Users/corneliusromer/.mambarc
                          /Users/corneliusromer/.condarc
       virtual packages : __unix=0=0
                          __osx=15.0=0
                          __archspec=1=arm64
               channels : https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/bioconda/osx-arm64
                          https://conda.anaconda.org/nodefaults/noarch
                          https://conda.anaconda.org/nodefaults/osx-arm64
       base environment : /Users/corneliusromer/micromamba
               platform : osx-arm64

Logs

$ micromamba env -v

there's really nothing there, just empty output

environment.yml

NA

~/.condarc

āÆ cat ~/.condarc
always_yes: true
show_channel_urls: true
solver: libmamba
changeps1: False
channels:
  - bioconda
  - conda-forge
  - nodefaults
channel_priority: strict

~ via šŸ v3.11.9 in ā˜ø aws (main) on ā˜ļø  (us-east-1)
āÆ cat ~/.mambarc
repodata_use_zst: true
channels:
- conda-forge
- bioconda
corneliusroemer commented 2 days ago

Possibly related: https://github.com/mamba-org/mamba/issues/3492

Also, as a workaround, I get this when using micromamba env list instead of micromamba env:

āÆ micromamba env list
  Name                    Active  Path
ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€ā”€
                                  /Users/corneliusromer/Miniforge3
                                  /Users/corneliusromer/Miniforge3/conda-bld/simplejson_1719492293018/_build_env
                                  /Users/corneliusromer/code/conda-base/.dev-env
                                  /Users/corneliusromer/code/mamba/build/envs/test
                                  /Users/corneliusromer/code/ncov/.snakemake/conda/07c1d165d433e95e46312a0a1caaede5_
                                  /Users/corneliusromer/code/ncov/.snakemake/conda/1eb5c34cec2847056d159ebb3ba309a0_
  base                            /Users/corneliusromer/micromamba
  ail-typo                        /Users/corneliusromer/micromamba/envs/ail-typo
  augur                           /Users/corneliusromer/micromamba/envs/augur
  augur-dev                       /Users/corneliusromer/micromamba/envs/augur-dev
  augur-dev-arm                   /Users/corneliusromer/micromamba/envs/augur-dev-arm
  auspice                         /Users/corneliusromer/micromamba/envs/auspice
  basetest                        /Users/corneliusromer/micromamba/envs/basetest
  bioconda                        /Users/corneliusromer/micromamba/envs/bioconda
  bioconda-arm                    /Users/corneliusromer/micromamba/envs/bioconda-arm
  bioconda-arm64                  /Users/corneliusromer/micromamba/envs/bioconda-arm64
  bioconda-test                   /Users/corneliusromer/micromamba/envs/bioconda-test
  bioconda-utils                  /Users/corneliusromer/micromamba/envs/bioconda-utils
  biopython                       /Users/corneliusromer/micromamba/envs/biopython
  build-raxml                     /Users/corneliusromer/micromamba/envs/build-raxml
  cartopy                         /Users/corneliusromer/micromamba/envs/cartopy
  cdk8s                           /Users/corneliusromer/micromamba/envs/cdk8s
  ceri                            /Users/corneliusromer/micromamba/envs/ceri
  clangdev                        /Users/corneliusromer/micromamba/envs/clangdev
  cmaple                          /Users/corneliusromer/micromamba/envs/cmaple
  codespell                       /Users/corneliusromer/micromamba/envs/codespell
  default                         /Users/corneliusromer/micromamba/envs/default
  email-validator                 /Users/corneliusromer/micromamba/envs/email-validator
  ena-submission                  /Users/corneliusromer/micromamba/envs/ena-submission
  fh                              /Users/corneliusromer/micromamba/envs/fh
  fhdev                           /Users/corneliusromer/micromamba/envs/fhdev
  flu_frequencies                 /Users/corneliusromer/micromamba/envs/flu_frequencies
  flu_frequencies_test            /Users/corneliusromer/micromamba/envs/flu_frequencies_test
  gofasta                         /Users/corneliusromer/micromamba/envs/gofasta
  grayskull                       /Users/corneliusromer/micromamba/envs/grayskull
  hyphy                           /Users/corneliusromer/micromamba/envs/hyphy
  hyphy-x86                       /Users/corneliusromer/micromamba/envs/hyphy-x86
  iqtree                          /Users/corneliusromer/micromamba/envs/iqtree
  iqtree-cmaple                   /Users/corneliusromer/micromamba/envs/iqtree-cmaple
  iqtree-native                   /Users/corneliusromer/micromamba/envs/iqtree-native
  khipu                           /Users/corneliusromer/micromamba/envs/khipu
  lapis-silo                      /Users/corneliusromer/micromamba/envs/lapis-silo
  ldc                             /Users/corneliusromer/micromamba/envs/ldc
  loculus-ena                     /Users/corneliusromer/micromamba/envs/loculus-ena
  loculus-ena-submission          /Users/corneliusromer/micromamba/envs/loculus-ena-submission
  loculus-ingest                  /Users/corneliusromer/micromamba/envs/loculus-ingest
  loculus-nextclade               /Users/corneliusromer/micromamba/envs/loculus-nextclade
  loculus-submission              /Users/corneliusromer/micromamba/envs/loculus-submission
  lr_quant_benchmark              /Users/corneliusromer/micromamba/envs/lr_quant_benchmark
  mamba                           /Users/corneliusromer/micromamba/envs/mamba
  matchspec                       /Users/corneliusromer/micromamba/envs/matchspec
  miniwdl                         /Users/corneliusromer/micromamba/envs/miniwdl
  mpox-nextclade                  /Users/corneliusromer/micromamba/envs/mpox-nextclade
  nbdev                           /Users/corneliusromer/micromamba/envs/nbdev
  nbdevcf                         /Users/corneliusromer/micromamba/envs/nbdevcf
  nextclade                       /Users/corneliusromer/micromamba/envs/nextclade
  nextclade-data                  /Users/corneliusromer/micromamba/envs/nextclade-data
  nextclade-sc2                   /Users/corneliusromer/micromamba/envs/nextclade-sc2
  nextstrain-base                 /Users/corneliusromer/micromamba/envs/nextstrain-base
  nwkfmtdev                       /Users/corneliusromer/micromamba/envs/nwkfmtdev
  obecni                          /Users/corneliusromer/micromamba/envs/obecni
  osxtest                         /Users/corneliusromer/micromamba/envs/osxtest
  otd                             /Users/corneliusromer/micromamba/envs/otd
  pango3116                       /Users/corneliusromer/micromamba/envs/pango3116
  pango402                        /Users/corneliusromer/micromamba/envs/pango402
  pathoplexus-nextclade           /Users/corneliusromer/micromamba/envs/pathoplexus-nextclade
  pc                              /Users/corneliusromer/micromamba/envs/pc
  pl019                           /Users/corneliusromer/micromamba/envs/pl019
  polars                          /Users/corneliusromer/micromamba/envs/polars
  poseidon                        /Users/corneliusromer/micromamba/envs/poseidon
  pp-integrity                    /Users/corneliusromer/micromamba/envs/pp-integrity
  py12                    *       /Users/corneliusromer/micromamba/envs/py12
  py36-64                         /Users/corneliusromer/micromamba/envs/py36-64
  py38-test                       /Users/corneliusromer/micromamba/envs/py38-test
  py39-test                       /Users/corneliusromer/micromamba/envs/py39-test
  pypy-arm                        /Users/corneliusromer/micromamba/envs/pypy-arm
  raxml                           /Users/corneliusromer/micromamba/envs/raxml
  related-issues                  /Users/corneliusromer/micromamba/envs/related-issues
  repro_zipfile                   /Users/corneliusromer/micromamba/envs/repro_zipfile
  s7_32                           /Users/corneliusromer/micromamba/envs/s7_32
  s7_3_2                          /Users/corneliusromer/micromamba/envs/s7_3_2
  s7py11                          /Users/corneliusromer/micromamba/envs/s7py11
  s8_10                           /Users/corneliusromer/micromamba/envs/s8_10
  s8_10py11                       /Users/corneliusromer/micromamba/envs/s8_10py11
  s8_13py11                       /Users/corneliusromer/micromamba/envs/s8_13py11
  s8_16                           /Users/corneliusromer/micromamba/envs/s8_16
  s8_16py11                       /Users/corneliusromer/micromamba/envs/s8_16py11
  s8_17                           /Users/corneliusromer/micromamba/envs/s8_17
  s8_18                           /Users/corneliusromer/micromamba/envs/s8_18
  s8_18py11                       /Users/corneliusromer/micromamba/envs/s8_18py11
  s8_1py11                        /Users/corneliusromer/micromamba/envs/s8_1py11
  sdow-backend                    /Users/corneliusromer/micromamba/envs/sdow-backend
  silo                            /Users/corneliusromer/micromamba/envs/silo
  slack                           /Users/corneliusromer/micromamba/envs/slack
  smdpcli                         /Users/corneliusromer/micromamba/envs/smdpcli
  smithy                          /Users/corneliusromer/micromamba/envs/smithy
  snakemake                       /Users/corneliusromer/micromamba/envs/snakemake
  snakemake-dev                   /Users/corneliusromer/micromamba/envs/snakemake-dev
  snakemake-test                  /Users/corneliusromer/micromamba/envs/snakemake-test
  sreality                        /Users/corneliusromer/micromamba/envs/sreality
  test                            /Users/corneliusromer/micromamba/envs/test
  test1                           /Users/corneliusromer/micromamba/envs/test1
  throwaway                       /Users/corneliusromer/micromamba/envs/throwaway
  treetime                        /Users/corneliusromer/micromamba/envs/treetime
  trimadap                        /Users/corneliusromer/micromamba/envs/trimadap
  tsv-utils                       /Users/corneliusromer/micromamba/envs/tsv-utils
  tsv-utils-bioconda              /Users/corneliusromer/micromamba/envs/tsv-utils-bioconda
  usher                           /Users/corneliusromer/micromamba/envs/usher
  vcftools-build                  /Users/corneliusromer/micromamba/envs/vcftools-build
  xopen                           /Users/corneliusromer/micromamba/envs/xopen
  xopen-arm                       /Users/corneliusromer/micromamba/envs/xopen-arm
  zstdtest                        /Users/corneliusromer/micromamba/envs/zstdtest
                                  /opt/homebrew/Caskroom/miniforge/base
                                  /opt/homebrew/Caskroom/miniforge/base/envs/aliasor
                                  /opt/homebrew/Caskroom/miniforge/base/envs/augur-dev
                                  /opt/homebrew/Caskroom/miniforge/base/envs/auspice
                                  /opt/homebrew/Caskroom/miniforge/base/envs/auspice-dev
                                  /opt/homebrew/Caskroom/miniforge/base/envs/bioconda-64
                                  /opt/homebrew/Caskroom/miniforge/base/envs/conda-base
                                  /opt/homebrew/Caskroom/miniforge/base/envs/general
                                  /opt/homebrew/Caskroom/miniforge/base/envs/grayskullenv
                                  /opt/homebrew/Caskroom/miniforge/base/envs/mamba-dev
                                  /opt/homebrew/Caskroom/miniforge/base/envs/mambabug
                                  /opt/homebrew/Caskroom/miniforge/base/envs/managed-conda
                                  /opt/homebrew/Caskroom/miniforge/base/envs/matchspec
                                  /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain
                                  /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-base
                                  /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain-reinstall
                                  /opt/homebrew/Caskroom/miniforge/base/envs/opencv
                                  /opt/homebrew/Caskroom/miniforge/base/envs/pangolin
                                  /opt/homebrew/Caskroom/miniforge/base/envs/pangolinUsherSampled
                                  /opt/homebrew/Caskroom/miniforge/base/envs/polars-book
                                  /opt/homebrew/Caskroom/miniforge/base/envs/py11
                                  /opt/homebrew/Caskroom/miniforge/base/envs/py11-64
                                  /opt/homebrew/Caskroom/miniforge/base/envs/pyfastx
                                  /opt/homebrew/Caskroom/miniforge/base/envs/pypy
                                  /opt/homebrew/Caskroom/miniforge/base/envs/pypy-arm
                                  /opt/homebrew/Caskroom/miniforge/base/envs/pypy=7.3.11
                                  /opt/homebrew/Caskroom/miniforge/base/envs/r
                                  /opt/homebrew/Caskroom/miniforge/base/envs/snakefmt
                                  /opt/homebrew/Caskroom/miniforge/base/envs/snakemake
                                  /opt/homebrew/Caskroom/miniforge/base/envs/taxonium
                                  /opt/homebrew/Caskroom/miniforge/base/envs/testenv
                                  /opt/homebrew/Caskroom/miniforge/base/envs/treetime
                                  /opt/homebrew/Caskroom/miniforge/base/envs/treetime9
                                  /opt/homebrew/Caskroom/miniforge/base/envs/wf-artic
corneliusroemer commented 2 days ago

Maybe this "works as intended"?

The reason I expected micromamba env to show results is the help text:

$ micromamba -h
...
Subcommands:
...
  info                        Information about micromamba
  constructor                 Commands to support using micromamba in constructor
  env                         List environments
  activate                    Activate an environment
...

in particular the line:

  env                         List environments

It turns out that I think the expected command is indeed micromamba env list.

However, the issue is then that micromamba env should show usage information for micromamba env -h instead of just producing no output (which can be mistaken as "there are no environments")

jjerphan commented 2 days ago

See https://github.com/mamba-org/mamba/pull/3502.