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micromamba env does not show any environments in v2.0.2, despite having lots of environments #3500

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corneliusroemer opened this issue Oct 3, 2024 · 3 comments · May be fixed by #3502
Open
3 tasks done

micromamba env does not show any environments in v2.0.2, despite having lots of environments #3500

corneliusroemer opened this issue Oct 3, 2024 · 3 comments · May be fixed by #3502

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@corneliusroemer
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corneliusroemer commented Oct 3, 2024 •
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Troubleshooting docs

  • My problem is not solved in the Troubleshooting docs

Anaconda default channels

  • I do NOT use the Anaconda default channels (pkgs/* etc.)

How did you install Mamba?

Mambaforge or latest Miniforge

Search tried in issue tracker

micromamba env

Latest version of Mamba

  • My problem is not solved with the latest version

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 🐍 v3.11.9 in ☸ aws (main) on ☁️  (us-east-1)
❯ 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:

❯ micromamba activate py12

~ via 🐍 v3.12.6 in ☸ aws (main) via 🅒 py12 on ☁️  (us-east-1)
❯

mamba info / micromamba info

❯ 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

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

~ via 🐍 v3.11.9 in ☸ aws (main) on ☁️  (us-east-1)
❯ cat ~/.mambarc
repodata_use_zst: true
channels:
- conda-forge
- bioconda
@corneliusroemer
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Possibly related: #3492

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

❯ micromamba env list
  Name                    Active  Path
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
                                  /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
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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")

@corneliusroemer corneliusroemer changed the title micromamba env does not show any environments in v2.0.2 anymore, despite having lots of environments micromamba env does not show any environments in v2.0.2, despite having lots of environments Oct 3, 2024
@jjerphan jjerphan linked a pull request Oct 3, 2024 that will close this issue
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@jjerphan
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jjerphan commented Oct 3, 2024

See #3502.

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maint: Clarify env subcommand documentation in help menu jjerphan/mamba
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@jjerphan @corneliusroemer