conda shell function injects $CONDA_PREFIX into $PATH causing incorrect behavior in conda run #11174
Description
Description
What happened?
The $PATH/%PATH% set by conda run includes directories from the base environment; conda activate, on the other hand, removes base environment components from the PATH. This can be problematic, as conda run and conda activate can have different executables (and on Windows, DLLs) available to the user.
A basic replicating case:
(base) $ conda create -n py39 python=3.9
(base) $ conda run -n py39 python -c 'import os; print(os.environ["PATH"]);'
${CONDA_ROOT}/envs/py39/bin:${CONDA_ROOT}/bin:${CONDA_ROOT}/condabin:${HOME}/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
(base) $ conda activate py39
(py39) $ python -c 'import os; print(os.environ["PATH"]);'
${CONDA_ROOT}/envs/py39/bin:${CONDA_ROOT}/condabin:${HOME}/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
(Note that ${CONDA_ROOT}/bin gets removed from $PATH in the activated environment, but not when using conda run.)
Conda Details
conda info
active environment : base
active env location : ${CONDA_ROOT}
shell level : 1
user config file : ${HOME}/.condarc
populated config files : ${HOME}/.condarc
conda version : 4.11.0
conda-build version : 3.21.7
python version : 3.8.12.final.0
virtual packages : __osx=10.16=0
__unix=0=0
__archspec=1=x86_64
base environment : ${CONDA_ROOT} (writable)
conda av data dir : ${CONDA_ROOT}/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : ${CONDA_ROOT}/pkgs
${HOME}/.conda/pkgs
envs directories : ${CONDA_ROOT}/envs
${HOME}/.conda/envs
platform : osx-64
user-agent : conda/4.11.0 requests/2.27.1 CPython/3.8.12 Darwin/20.6.0 OSX/10.16
UID:GID : 502:20
netrc file : None
offline mode : Falseconda config
==> ${HOME}/.condarc <==
restore_free_channel: False
conda_build:
error_overdepending: True
error_overlinking: Trueconda list
# packages in environment at /Users/clee/Applications/miniconda3:
#
# Name Version Build Channel
anaconda-client 1.9.0 py38hecd8cb5_0 defaults
attrs 21.4.0 pyhd3eb1b0_0 defaults
beautifulsoup4 4.10.0 pyh06a4308_0 defaults
brotlipy 0.7.0 py38h9ed2024_1003 defaults
bzip2 1.0.8 h1de35cc_0 defaults
ca-certificates 2021.10.26 hecd8cb5_2 defaults
certifi 2021.10.8 py38hecd8cb5_2 defaults
cffi 1.15.0 py38hc55c11b_1 defaults
chardet 4.0.0 py38hecd8cb5_1003 defaults
charset-normalizer 2.0.4 pyhd3eb1b0_0 defaults
clyent 1.2.2 py38_1 defaults
conda 4.11.0 py38hecd8cb5_0 defaults
conda-build 3.21.7 py38hecd8cb5_0 defaults
conda-content-trust 0.1.1 pyhd3eb1b0_0 defaults
conda-package-handling 1.7.3 py38h9ed2024_1 defaults
conda-token 0.3.0 pyhd3eb1b0_0 defaults
coreutils 8.32 haf1e3a3_0 defaults
cryptography 36.0.0 py38hf6deb26_0 defaults
filelock 3.4.2 pyhd3eb1b0_0 defaults
glob2 0.7 pyhd3eb1b0_0 defaults
icu 58.2 h0a44026_3 defaults
idna 3.3 pyhd3eb1b0_0 defaults
importlib-metadata 4.8.2 py38hecd8cb5_0 defaults
importlib_metadata 4.8.2 hd3eb1b0_0 defaults
ipython_genutils 0.2.0 pyhd3eb1b0_1 defaults
jinja2 2.11.3 pyhd3eb1b0_0 defaults
jq 1.6 h9ed2024_1000 defaults
jsonschema 3.2.0 pyhd3eb1b0_2 defaults
jupyter_core 4.9.1 py38hecd8cb5_0 defaults
libarchive 3.4.2 ha0e9c3a_0 defaults
libcxx 12.0.0 h2f01273_0 defaults
libffi 3.3 hb1e8313_2 defaults
libiconv 1.16 h1de35cc_0 defaults
liblief 0.10.1 h0a44026_0 defaults
libxml2 2.9.12 hcdb78fc_0 defaults
lz4-c 1.9.3 h23ab428_1 defaults
markupsafe 2.0.1 py38h9ed2024_0 defaults
nbformat 5.1.3 pyhd3eb1b0_0 defaults
ncurses 6.3 hca72f7f_2 defaults
oniguruma 6.9.7.1 h9ed2024_0 defaults
openssl 1.1.1m hca72f7f_0 defaults
packaging 21.3 pyhd3eb1b0_0 defaults
pip 21.2.4 py38hecd8cb5_0 defaults
pkginfo 1.8.2 pyhd3eb1b0_0 defaults
psutil 5.8.0 py38h9ed2024_1 defaults
py-lief 0.10.1 py38haf313ee_0 defaults
pycosat 0.6.3 py38h1de35cc_1 defaults
pycparser 2.21 pyhd3eb1b0_0 defaults
pyopenssl 21.0.0 pyhd3eb1b0_1 defaults
pyparsing 3.0.4 pyhd3eb1b0_0 defaults
pyrsistent 0.18.0 py38hca72f7f_0 defaults
pysocks 1.7.1 py38_1 defaults
python 3.8.12 h88f2d9e_0 defaults
python-dateutil 2.8.2 pyhd3eb1b0_0 defaults
python-libarchive-c 2.9 pyhd3eb1b0_1 defaults
python.app 3 py38hca72f7f_0 defaults
pytz 2021.3 pyhd3eb1b0_0 defaults
pyyaml 6.0 py38hca72f7f_1 defaults
readline 8.1.2 hca72f7f_1 defaults
requests 2.27.1 pyhd3eb1b0_0 defaults
ripgrep 12.1.1 0 defaults
ruamel.yaml 0.16.12 py38haf1e3a3_1 defaults
ruamel.yaml.clib 0.2.6 py38hca72f7f_0 defaults
ruamel_yaml 0.15.100 py38h9ed2024_0 defaults
setuptools 58.0.4 py38hecd8cb5_0 defaults
six 1.16.0 pyhd3eb1b0_0 defaults
soupsieve 2.3.1 pyhd3eb1b0_0 defaults
sqlite 3.37.0 h707629a_0 defaults
tk 8.6.11 h7bc2e8c_0 defaults
tqdm 4.62.3 pyhd3eb1b0_1 defaults
traitlets 5.1.1 pyhd3eb1b0_0 defaults
urllib3 1.26.7 pyhd3eb1b0_0 defaults
wget 1.20.1 h051b688_0 defaults
wheel 0.37.1 pyhd3eb1b0_0 defaults
xz 5.2.5 h1de35cc_0 defaults
yaml 0.2.5 haf1e3a3_0 defaults
zipp 3.7.0 pyhd3eb1b0_0 defaults
zlib 1.2.11 h4dc903c_4 defaults
zstd 1.5.0 hcb37349_1 defaults
Resolution
It would appear that the __add_sys_prefix_to_path shell function added in conda 4.6.12 is the culprit here.
Duplicate Issues
- Running using
conda runinside already activated environment should be the same as running it outside #11305 - conda run -n MY-ENV python FILE.py uses the base interpreter instead of environment interpreter. #9587
conda runsometimes uses python in the base environment #8450- Different basic environment activate the same environment but lead to different places #10786
- conda run python in it's own activated environment not using proper python #9571
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if an issue/PR has duplicates, this is the consolidated, primary issue/PRissue is actively being worked on[bot] locked due to inactivitypertains to conda-runblocker; broken functionality with no workaroundcreated by members of Anaconda, Inc.catch-all for issues filed by community membersdescribes erroneous operation, use severity::* to classify the type
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