conda install -n base --revision 1 doesn't clean up pypi packages

Question

I attempted cleaning up my base (mini)conda environment by installing revision 1 of the base environment.

$ conda install -n base --revision 1

For reference, here is what revision 1 means in my case.

$ conda list -n base --revisions
2019-10-24 14:29:57  (rev 0)
    +asn1crypto-1.2.0
    +ca-certificates-2019.10.16
    +certifi-2019.9.11
    +cffi-1.13.0
    +chardet-3.0.4
    +conda-4.7.12
    +conda-package-handling-1.6.0
    +cryptography-2.8
    +idna-2.8
    +libcxx-4.0.1
    +libcxxabi-4.0.1
    +libedit-3.1.20181209
    +libffi-3.2.1
    +ncurses-6.1
    +openssl-1.1.1d
    +pip-19.3.1
    +pycosat-0.6.3
    +pycparser-2.19
    +pyopenssl-19.0.0
    +pysocks-1.7.1
    +python-3.7.4
    +python.app-2
    +readline-7.0
    +requests-2.22.0
    +ruamel_yaml-0.15.46
    +setuptools-41.4.0
    +six-1.12.0
    +sqlite-3.30.0
    +tk-8.6.8
    +tqdm-4.36.1
    +urllib3-1.24.2
    +wheel-0.33.6
    +xz-5.2.4
    +yaml-0.1.7
    +zlib-1.2.11

2019-11-06 20:50:32  (rev 1)
     cffi  {1.13.0 -> 1.13.1}
     setuptools  {41.4.0 -> 41.6.0}
     sqlite  {3.30.0 -> 3.30.1}

Despite the above conda install command, my base environment is still polluted by various python packages, that were installed after revision 1.

$ conda list -n base
# packages in environment at /opt/miniconda3:
#
# Name                    Version                   Build  Channel
absl-py                   0.8.1                    pypi_0    pypi
alabaster                 0.7.12                   pypi_0    pypi
appnope                   0.1.0                    pypi_0    pypi
asn1crypto                1.2.0                    py37_0  
astor                     0.8.0                    pypi_0    pypi
aws-sam-translator        1.21.0                   pypi_0    pypi
aws-xray-sdk              2.4.3                    pypi_0    pypi
babel                     2.8.0                    pypi_0    pypi
bleach                    3.1.0                    pypi_0    pypi
boto                      2.49.0                   pypi_0    pypi
boto3                     1.12.17                  pypi_0    pypi
botocore                  1.15.17                  pypi_0    pypi
ca-certificates           2019.10.16                    0  
certifi                   2019.9.11                py37_0  
cffi                      1.13.1           py37hb5b8e2f_0  
cfn-lint                  0.28.4                   pypi_0    pypi
chardet                   3.0.4                 py37_1003  
conda                     4.7.12                   py37_0  
conda-package-handling    1.6.0            py37h1de35cc_0  
confluence-py             1.0.1                    pypi_0    pypi
coverage                  5.0.3                    pypi_0    pypi
cryptography              2.8              py37ha12b0ac_0  
defusedxml                0.6.0                    pypi_0    pypi
docker                    4.2.0                    pypi_0    pypi
docutils                  0.16                     pypi_0    pypi
ecdsa                     0.15                     pypi_0    pypi
entrypoints               0.3                      pypi_0    pypi
future                    0.18.2                   pypi_0    pypi
gast                      0.2.2                    pypi_0    pypi
google-pasta              0.1.8                    pypi_0    pypi
grpcio                    1.24.3                   pypi_0    pypi
h5py                      2.8.0                    pypi_0    pypi
idna                      2.8                      py37_0  
imagesize                 1.2.0                    pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
jmespath                  0.9.5                    pypi_0    pypi
jsondiff                  1.1.2                    pypi_0    pypi
jsonpatch                 1.25                     pypi_0    pypi
jsonpickle                1.3                      pypi_0    pypi
jsonpointer               2.0                      pypi_0    pypi
jupyterlab                1.2.1                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.0                    pypi_0    pypi
libcxx                    4.0.1                hcfea43d_1  
libcxxabi                 4.0.1                hcfea43d_1  
libedit                   3.1.20181209         hb402a30_0  
libffi                    3.2.1                h475c297_4  
markdown                  3.1.1                    pypi_0    pypi
mock                      4.0.1                    pypi_0    pypi
moto                      1.3.14                   pypi_0    pypi
nbsphinx                  0.5.1                    pypi_0    pypi
ncurses                   6.1                  h0a44026_1  
numpy                     1.16.4                   pypi_0    pypi
openssl                   1.1.1d               h1de35cc_3  
opt-einsum                3.1.0                    pypi_0    pypi
packaging                 20.3                     pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pip                       19.3.1                   py37_0  
pluggy                    0.13.1                   pypi_0    pypi
protobuf                  3.10.0                   pypi_0    pypi
ptyprocess                0.6.0                    pypi_0    pypi
py                        1.8.1                    pypi_0    pypi
pyasn1                    0.4.8                    pypi_0    pypi
pycosat                   0.6.3            py37h1de35cc_0  
pycparser                 2.19                     py37_0  
pyflakes                  2.1.1                    pypi_0    pypi
pyinquirer                1.0.3                    pypi_0    pypi
pyopenssl                 19.0.0                   py37_0  
pyparsing                 2.4.6                    pypi_0    pypi
pyrsistent                0.15.5                   pypi_0    pypi
pysocks                   1.7.1                    py37_0  
pytest                    5.3.5                    pypi_0    pypi
pytest-cov                2.8.1                    pypi_0    pypi
pytest-flakes             4.0.0                    pypi_0    pypi
python                    3.7.4                h359304d_1  
python-jose               3.1.0                    pypi_0    pypi
python.app                2                        py37_9  
pytz                      2019.3                   pypi_0    pypi
pyyaml                    5.3                      pypi_0    pypi
pyzmq                     18.1.0                   pypi_0    pypi
readline                  7.0                  h1de35cc_5  
regex                     2019.11.1                pypi_0    pypi
requests                  2.22.0                   py37_0  
responses                 0.10.12                  pypi_0    pypi
rsa                       4.0                      pypi_0    pypi
ruamel_yaml               0.15.46          py37h1de35cc_0  
s3transfer                0.3.3                    pypi_0    pypi
send2trash                1.5.0                    pypi_0    pypi
setuptools                41.6.0                   py37_0  
six                       1.11.0                   pypi_0    pypi
snowballstemmer           2.0.0                    pypi_0    pypi
sphinx                    2.4.4                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    1.0.3                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.4                    pypi_0    pypi
sqlite                    3.30.1               ha441bb4_0  
sshpubkeys                3.1.0                    pypi_0    pypi
tensorboard               1.15.0                   pypi_0    pypi
tensorflow                1.15.0                   pypi_0    pypi
tensorflow-estimator      1.15.1                   pypi_0    pypi
tensorflow-hub            0.5.0                    pypi_0    pypi
tensorflowjs              1.3.1.1                  pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
terminado                 0.8.2                    pypi_0    pypi
tk                        8.6.8                ha441bb4_0  
tqdm                      4.36.1                     py_0  
urllib3                   1.24.2                   py37_0  
wcwidth                   0.1.7                    pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          0.57.0                   pypi_0    pypi
werkzeug                  0.16.0                   pypi_0    pypi
wheel                     0.33.6                   py37_0  
wrapt                     1.11.2                   pypi_0    pypi
xmltodict                 0.12.0                   pypi_0    pypi
xz                        5.2.4                h1de35cc_4  
yaml                      0.1.7                hc338f04_2  
zlib                      1.2.11               h1de35cc_3

The environment still contains unwanted packages from the pypi channel. Can I only get rid of them via pip uninstall (which is terribly tedious) or there's a nicer / less manual way, like conda install --revision?

I would recommend removing and reinstalling Miniconda, so as to avoid any issues. Needless to say, using pip when it isn't necessary is a bad idea, and so is using the base environment for development. — AMC, Sep 01 '20 at 20:48

score 3 · Accepted Answer · answered Sep 01 '20 at 06:36

3

There is nothing in the Conda CLI to handle this, but pip uninstall also works with a requirements.txt, which could easily be made with this output. For example,

conda list | awk '$4 ~ /^pypi$/ { print $1 }' > requirements.txt
pip uninstall -r requirements.txt

or if you want a one liner

# make sure you have the right environment activated!
pip uninstall -r <(conda list | awk '$4 ~ /^pypi$/ {print $1}')

There is a -y flag for pip uninstall, but I would review the operation, just to double check it is removing from where you expect.

answered Sep 01 '20 at 06:36

merv

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1

On spot, thank you @merv. The only issue, which is slightly related to the question is that the environment contains packages that have an empty channel, yet shouldn't be part of the base "naked" environment, like `cryptography`, `idna`, `tqdm`, ... – honestly I don't even know which shouldn't be there and which shoul. I have no clue the source of the installation of this, honestly. _Anyway your answer helps with automating the deletion, thanks a lot!_ – borosdenes Sep 01 '20 at 17:24
I think the "naked" environment would correspond to revision 0 instead of 1. – merv Sep 01 '20 at 18:50
Interestingly some non-standard packages are already included in revision 0, that seems odd to me. Anyways, installing revision 0 is [highly discouraged as it may break the conda installation](https://stackoverflow.com/a/52841447/5525075). But once again, my base is now clean enough thanks to the above pipe based solution. – borosdenes Sep 01 '20 at 19:09
1

Actually I was mistaken, `tqdm` and such (those which I listed before) are included in the base environment even if after I reinstalled conda (miniconda, more precisely). – borosdenes Sep 01 '20 at 19:58
1

Very very interesting and elegant. Thanks a lot. Works well with my conda env on Mac with apple silicon. – Robert Alexander Dec 06 '22 at 09:35

conda install -n base --revision 1 doesn't clean up pypi packages

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