No Hardlinks upon environment clone and update / during Docker build

[creative-resort]

Troubleshooting docs

• [X] My problem is not solved in the Troubleshooting docs

Anaconda default channels

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

How did you install Mamba?

Micromamba

Search tried in issue tracker

docker clone hardlink

Latest version of Mamba

• [X] My problem is not solved with the latest version

Tried in Conda?

Not applicable

Describe your issue

When I clone the base environment and in the same line update it with additional dependencies, that overlap with the base env (environment.txt contains some of the same packages as already installed in base, using plain package names without versions) as follows:

mamba create --clone base -n "pythondev" --file environment.txt

The new environment "pythondev" has no hardlinks to the base environment but adds to the disk usage with full weight.

I'm running this to build a Docker Image and need to keep that as slim as possible. What am I doing wrong, or is this an insufficiency of mamba?

mamba info / micromamba info

mamba version : 1.5.9
     active environment : pythondev
    active env location : /opt/conda/envs/pythondev
            shell level : 2
       user config file : /home/jovyan/.condarc
 populated config files : /opt/conda/.condarc
                          /opt/conda/envs/pythondev/.condarc
          conda version : 24.7.1
    conda-build version : not installed
         python version : 3.11.9.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=nehalem
                          __conda=24.7.1=0
                          __glibc=2.39=0
                          __linux=5.10.0=0
                          __unix=0=0
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /opt/conda/pkgs
                          /home/jovyan/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/jovyan/.conda/envs
               platform : linux-64
             user-agent : conda/24.7.1 requests/2.32.3 CPython/3.11.9 Linux/5.10.0-19-amd64 ubuntu/24.04.1 glibc/2.39 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.9
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Logs

No response

environment.yml

numpy
pandas
scikit-learn
matplotlib
seaborn
plotly

~/.condarc

No response