Pruning environment from yaml file doesn't respect pip changes

[marcelned]

Environment:

• mamba 0.19.0
• conda 4.11.0

Issue:

# environment.yaml
name: test
dependencies:
  - numpy
  - pip
  - pip:
    - pandas

$ mamba env create -f environment.yml
$ mamba list -n test

# Name                    Version                   Build  Channel
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
libblas                   3.9.0           12_osx64_openblas    conda-forge
libcblas                  3.9.0           12_osx64_openblas    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
liblapack                 3.9.0           12_osx64_openblas    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
llvm-openmp               12.0.1               hda6cdc1_1    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
numpy                     1.21.4          py310hd5a656b_0    conda-forge
openssl                   3.0.0                h0d85af4_2    conda-forge
pandas                    1.3.4                    pypi_0    pypi
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
python                    3.10.0          h38b4d05_3_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.10                    2_cp310    conda-forge
pytz                      2021.3                   pypi_0    pypi
readline                  8.1                  h05e3726_0    conda-forge
setuptools                59.4.0          py310h2ec42d9_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sqlite                    3.37.0               h23a322b_0    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge

Now say we want to change some pip packages, adding scipy and removing pandas:

# environment.yaml
name: test
dependencies:
  - numpy
  - pip
  - pip:
    - scipy

$ mamba env update --name test -f environment.yml --prune
$ mamba list -n test

# Name                    Version                   Build  Channel
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
libblas                   3.9.0           12_osx64_openblas    conda-forge
libcblas                  3.9.0           12_osx64_openblas    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
liblapack                 3.9.0           12_osx64_openblas    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
llvm-openmp               12.0.1               hda6cdc1_1    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
numpy                     1.21.4          py310hd5a656b_0    conda-forge
openssl                   3.0.0                h0d85af4_2    conda-forge
pandas                    1.3.4                    pypi_0    pypi
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
python                    3.10.0          h38b4d05_3_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.10                    2_cp310    conda-forge
pytz                      2021.3                   pypi_0    pypi
readline                  8.1                  h05e3726_0    conda-forge
scipy                     1.7.3                    pypi_0    pypi
setuptools                59.4.0          py310h2ec42d9_0    conda-forge
six                       1.16.0                   pypi_0    pypi
sqlite                    3.37.0               h23a322b_0    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge

pandas has not been removed.

[baszalmstra]

Does this work for regular conda package?

[marcelned]

After testing with conda, the same issue pops up. Should this issue rather be posted on the conda repo?

[adament]

This does not even work if you remove conda packages see the weirdly named issue #688 for mamba and conda/conda#7279.