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The Fast Cross-Platform Package Manager
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Specs shown when running `micromamba create` do not show pip dependencies specified in environment.yaml #3343

Open corneliusroemer opened 1 month ago

corneliusroemer commented 1 month ago

Troubleshooting docs

Anaconda default channels

How did you install Mamba?

Mambaforge or latest Miniforge

Search tried in issue tracker

pip spec

Latest version of Mamba

Tried in Conda?

I didn't try

Describe your issue

My environment.yaml contains a pip section, e.g.:

name: ingest
channels:
  - conda-forge
dependencies:
  # Core Python dependencies
  - python =3.12
  - pip:
    - orjsonl

When I run:

micromamba create -n ingest -f environment.yml

The specs do not mention the pip-installed package at all:

❯ micromamba create -n ingest -f environment.yml
conda-forge/osx-64                                          Using cache
conda-forge/noarch                                          Using cache

Transaction

  Prefix: /Users/corneliusromer/micromamba/envs/loculus-ingest

  Updating specs:

   - python=3.12
   - pip

I would expect the specs to include the pip dependencies - otherwise the specs are incomplete.

mamba info / micromamba info

micromamba info                                                                            

       libmamba version : 1.5.8
     micromamba version : 1.5.8
           curl version : libcurl/8.6.0 (SecureTransport) LibreSSL/3.3.6 zlib/1.2.12 nghttp2/1.61.0
     libarchive version : libarchive 3.5.3 zlib/1.2.12 liblzma/5.4.3 bz2lib/1.0.8
       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=14.5=0
                          __archspec=1=arm64
               channels : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/osx-arm64
                          https://conda.anaconda.org/bioconda/noarch
       base environment : /Users/corneliusromer/micromamba
               platform : osx-arm64

Logs

No response

environment.yml

No response

~/.condarc

$ cat ~/.condarc                                          
always_yes: true
show_channel_urls: true
solver: libmamba
changeps1: False

$ cat ~/.mambarc
repodata_use_zst: true
channels:
- conda-forge
- bioconda