Conda: Can't execute `conda activate` from bash script
Current Behavior
Trying to use conda activate my_env does not work inside a bash script. The workaround is to use source activate my_env but this shouldn't be necessary.
Steps to Reproduce
Write a bash script with the following code inside, let's call it my-script.sh:
conda activate my_env
When you run ./my-script.sh, you get the following output:
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with
$ echo ". /Users/matthewspeck/anaconda3/etc/profile.d/conda.sh" >> ~/.bash_profile
or, for all users, enable conda with
$ sudo ln -s /Users/matthewspeck/anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh
The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH. To do so, run
$ conda activate
in your terminal, or to put the base environment on PATH permanently, run
$ echo "conda activate" >> ~/.bash_profile
Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bash_profile file. You should manually remove the line that looks like
export PATH="/Users/matthewspeck/anaconda3/bin:$PATH"
^^^ The above line should NO LONGER be in your ~/.bash_profile file! ^^^
However, conda is in fact installed correctly, and runs fine in the command line.
The command which conda returns the following:
conda () {
if [ "$#" -lt 1 ]
then
$_CONDA_EXE
else
\local cmd="$1"
shift
case "$cmd" in
(activate) _conda_activate "$@" ;;
(deactivate) _conda_deactivate "$@" ;;
(install | update | uninstall | remove) $_CONDA_EXE "$cmd" "$@" && _conda_reactivate ;;
(*) $_CONDA_EXE "$cmd" "$@" ;;
esac
fi
}
Expected Behavior
conda should activate in a bash script the same way it does on the command line.
Environment Information
conda info
active environment : base
active env location : /Users/matthewspeck/anaconda3
shell level : 1
user config file : /Users/matthewspeck/.condarc
populated config files : /Users/matthewspeck/.condarc
conda version : 4.5.11
conda-build version : 3.16.2
python version : 3.6.6.final.0
base environment : /Users/matthewspeck/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/osx-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/osx-64
https://repo.anaconda.com/pkgs/pro/noarch
package cache : /Users/matthewspeck/anaconda3/pkgs
/Users/matthewspeck/.conda/pkgs
envs directories : /Users/matthewspeck/anaconda3/envs
/Users/matthewspeck/.conda/envs
platform : osx-64
user-agent : conda/4.5.11 requests/2.20.0 CPython/3.6.6 Darwin/17.7.0 OSX/10.13.6
UID:GID : 501:20
netrc file : None
offline mode : False
conda config --show-sources
==> /Users/matthewspeck/.condarc <==
ssl_verify: True
channels:
- defaults
conda list --show-channel-urls
# packages in environment at /Users/matthewspeck/anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py36_0 defaults
alabaster 0.7.12 py36_0 defaults
anaconda-client 1.7.2 py36_0 defaults
anaconda-navigator 1.9.2 py36_0 defaults
anaconda-project 0.8.2 py36_0 defaults
appdirs 1.4.3 py36h28b3542_0 defaults
appnope 0.1.0 py36hf537a9a_0 defaults
appscript 1.0.1 py36h1de35cc_1 defaults
asn1crypto 0.24.0 py36_0 defaults
astroid 2.0.4 py36_0 defaults
astropy 3.0.5 py36h1de35cc_0 defaults
atomicwrites 1.2.1 py36_0 defaults
attrs 18.2.0 py36h28b3542_0 defaults
automat 0.7.0 py36_0 defaults
babel 2.6.0 py36_0 defaults
backcall 0.1.0 py36_0 defaults
backports 1.0 py36_1 defaults
backports.os 0.1.1 py36_0 defaults
backports.shutil_get_terminal_size 1.0.0 py36_2 defaults
beautifulsoup4 4.6.3 py36_0 defaults
bitarray 0.8.3 py36h1de35cc_0 defaults
bkcharts 0.2 py36h073222e_0 defaults
blas 1.0 mkl defaults
blaze 0.11.3 py36_0 defaults
bleach 3.0.2 py36_0 defaults
blosc 1.14.4 hd9629dc_0 defaults
bokeh 1.0.1 py36_0 defaults
boto 2.49.0 py36_0 defaults
bottleneck 1.2.1 py36h1d22016_1 defaults
bzip2 1.0.6 h1de35cc_5 defaults
ca-certificates 2018.03.07 0 defaults
certifi 2018.10.15 py36_0 defaults
cffi 1.11.5 py36h6174b99_1 defaults
chardet 3.0.4 py36_1 defaults
click 7.0 py36_0 defaults
cloudpickle 0.6.1 py36_0 defaults
clyent 1.2.2 py36_1 defaults
colorama 0.4.0 py36_0 defaults
conda 4.5.11 py36_0 defaults
conda-build 3.16.2 py36_0 defaults
conda-env 2.6.0 1 defaults
constantly 15.1.0 py36h28b3542_0 defaults
contextlib2 0.5.5 py36hd66e5e7_0 defaults
coverage 4.5.1 py36h1de35cc_0 defaults
cryptography 2.3.1 py36hdbc3d79_0 defaults
curl 7.61.0 ha441bb4_0 defaults
cycler 0.10.0 py36hfc81398_0 defaults
cython 0.29 py36h0a44026_0 defaults
cytoolz 0.9.0.1 py36h1de35cc_1 defaults
dask 0.20.0 py36_0 defaults
dask-core 0.20.0 py36_0 defaults
datashape 0.5.4 py36_1 defaults
dbus 1.13.2 h760590f_1 defaults
decorator 4.3.0 py36_0 defaults
defusedxml 0.5.0 py36_1 defaults
distributed 1.24.0 py36_0 defaults
docutils 0.14 py36hbfde631_0 defaults
entrypoints 0.2.3 py36_2 defaults
et_xmlfile 1.0.1 py36h1315bdc_0 defaults
expat 2.2.6 h0a44026_0 defaults
fastcache 1.0.2 py36h1de35cc_2 defaults
filelock 3.0.10 py36_0 defaults
flask 1.0.2 py36_1 defaults
flask-cors 3.0.6 py36_0 defaults
freetype 2.9.1 hb4e5f40_0 defaults
get_terminal_size 1.0.0 h7520d66_0 defaults
gettext 0.19.8.1 h15daf44_3 defaults
gevent 1.3.7 py36h1de35cc_1 defaults
glib 2.56.2 hd9629dc_0 defaults
glob2 0.6 py36_1 defaults
gmp 6.1.2 hb37e062_1 defaults
gmpy2 2.0.8 py36h6ef4df4_2 defaults
greenlet 0.4.15 py36h1de35cc_0 defaults
h5py 2.8.0 py36h878fce3_3 defaults
hdf5 1.10.2 hfa1e0ec_1 defaults
heapdict 1.0.0 py36_2 defaults
html5lib 1.0.1 py36_0 defaults
hyperlink 18.0.0 py36_0 defaults
icu 58.2 h4b95b61_1 defaults
idna 2.7 py36_0 defaults
imageio 2.4.1 py36_0 defaults
imagesize 1.1.0 py36_0 defaults
importlib_metadata 0.6 py36_0 defaults
incremental 17.5.0 py36_0 defaults
intel-openmp 2019.0 118 defaults
ipykernel 5.1.0 py36h39e3cac_0 defaults
ipython 7.1.1 py36h39e3cac_0 defaults
ipython_genutils 0.2.0 py36h241746c_0 defaults
ipywidgets 7.4.2 py36_0 defaults
isort 4.3.4 py36_0 defaults
itsdangerous 1.1.0 py36_0 defaults
jbig 2.1 h4d881f8_0 defaults
jdcal 1.4 py36_0 defaults
jedi 0.13.1 py36_0 defaults
jinja2 2.10 py36_0 defaults
jpeg 9b he5867d9_2 defaults
jsonschema 2.6.0 py36hb385e00_0 defaults
jupyter 1.0.0 py36_7 defaults
jupyter_client 5.2.3 py36_0 defaults
jupyter_console 6.0.0 py36_0 defaults
jupyter_core 4.4.0 py36_0 defaults
jupyterlab 0.35.3 py36_0 defaults
jupyterlab_launcher 0.13.1 py36_0 defaults
jupyterlab_server 0.2.0 py36_0 defaults
keyring 16.0.0 py36_0 defaults
kiwisolver 1.0.1 py36h0a44026_0 defaults
lazy-object-proxy 1.3.1 py36h1de35cc_2 defaults
libarchive 3.3.3 hc2e69e3_1 defaults
libcurl 7.61.0 hf30b1f0_0 defaults
libcxx 4.0.1 h579ed51_0 defaults
libcxxabi 4.0.1 hebd6815_0 defaults
libedit 3.1.20170329 hb402a30_2 defaults
libffi 3.2.1 h475c297_4 defaults
libgfortran 3.0.1 h93005f0_2 defaults
libiconv 1.15 hdd342a3_7 defaults
libpng 1.6.34 he12f830_0 defaults
libsodium 1.0.16 h3efe00b_0 defaults
libssh2 1.8.0 h322a93b_4 defaults
libtiff 4.0.9 hcb84e12_2 defaults
libxml2 2.9.8 hab757c2_1 defaults
libxslt 1.1.32 hb819dd2_0 defaults
llvmlite 0.25.0 py36h8c7ce04_0 defaults
locket 0.2.0 py36hca03003_1 defaults
lxml 4.2.5 py36hef8c89e_0 defaults
lz4-c 1.8.1.2 h1de35cc_0 defaults
lzo 2.10 h362108e_2 defaults
markupsafe 1.0 py36h1de35cc_1 defaults
matplotlib 3.0.0 py36h54f8f79_0 defaults
mccabe 0.6.1 py36_1 defaults
mistune 0.8.4 py36h1de35cc_0 defaults
mkl 2019.0 118 defaults
mkl-service 1.1.2 py36h6b9c3cc_5 defaults
mkl_fft 1.0.6 py36hb8a8100_0 defaults
mkl_random 1.0.1 py36h5d10147_1 defaults
more-itertools 4.3.0 py36_0 defaults
mpc 1.1.0 h6ef4df4_1 defaults
mpfr 4.0.1 h3018a27_3 defaults
mpmath 1.0.0 py36_2 defaults
msgpack-python 0.5.6 py36h04f5b5a_1 defaults
multipledispatch 0.6.0 py36_0 defaults
navigator-updater 0.2.1 py36_0 defaults
nbconvert 5.4.0 py36_1 defaults
nbformat 4.4.0 py36h827af21_0 defaults
ncurses 6.1 h0a44026_0 defaults
networkx 2.2 py36_1 defaults
nltk 3.3.0 py36_0 defaults
nose 1.3.7 py36_2 defaults
notebook 5.7.0 py36_0 defaults
numba 0.40.0 py36h6440ff4_0 defaults
numexpr 2.6.8 py36h1dc9127_0 defaults
numpy 1.15.4 py36h6a91979_0 defaults
numpy-base 1.15.4 py36h8a80b8c_0 defaults
numpydoc 0.8.0 py36_0 defaults
odo 0.5.1 py36hc1af34a_0 defaults
olefile 0.46 py36_0 defaults
openpyxl 2.5.9 py36_0 defaults
openssl 1.0.2p h1de35cc_0 defaults
packaging 18.0 py36_0 defaults
pandas 0.23.4 py36h6440ff4_0 defaults
pandoc 1.19.2.1 ha5e8f32_1 defaults
pandocfilters 1.4.2 py36_1 defaults
parso 0.3.1 py36_0 defaults
partd 0.3.9 py36_0 defaults
path.py 11.5.0 py36_0 defaults
pathlib2 2.3.2 py36_0 defaults
patsy 0.5.1 py36_0 defaults
pcre 8.42 h378b8a2_0 defaults
pep8 1.7.1 py36_0 defaults
pexpect 4.6.0 py36_0 defaults
pickleshare 0.7.5 py36_0 defaults
pillow 5.3.0 py36hb68e598_0 defaults
pip 18.1 py36_0 defaults
pkginfo 1.4.2 py36_1 defaults
pluggy 0.8.0 py36_0 defaults
ply 3.11 py36_0 defaults
prometheus_client 0.4.2 py36_0 defaults
prompt_toolkit 2.0.7 py36_0 defaults
psutil 5.4.8 py36h1de35cc_0 defaults
ptyprocess 0.6.0 py36_0 defaults
py 1.7.0 py36_0 defaults
pyasn1 0.4.4 py36h28b3542_0 defaults
pyasn1-modules 0.2.2 py36_0 defaults
pycodestyle 2.4.0 py36_0 defaults
pycosat 0.6.3 py36h1de35cc_0 defaults
pycparser 2.19 py36_0 defaults
pycrypto 2.6.1 py36h1de35cc_9 defaults
pycurl 7.43.0.2 py36hdbc3d79_0 defaults
pyflakes 2.0.0 py36_0 defaults
pygments 2.2.0 py36h240cd3f_0 defaults
pylint 2.1.1 py36_0 defaults
pyodbc 4.0.24 py36h0a44026_0 defaults
pyopenssl 18.0.0 py36_0 defaults
pyparsing 2.3.0 py36_0 defaults
pyqt 5.9.2 py36h655552a_2 defaults
pysocks 1.6.8 py36_0 defaults
pytables 3.4.4 py36h13cba08_0 defaults
pytest 3.10.0 py36_0 defaults
pytest-arraydiff 0.2 py36h39e3cac_0 defaults
pytest-astropy 0.4.0 py36_0 defaults
pytest-cov 2.6.0 py36_0 defaults
pytest-doctestplus 0.1.3 py36_0 defaults
pytest-openfiles 0.3.0 py36_0 defaults
pytest-remotedata 0.3.1 py36_0 defaults
python 3.6.6 hc167b69_0 defaults
python-dateutil 2.7.5 py36_0 defaults
python-libarchive-c 2.8 py36_6 defaults
python.app 2 py36_9 defaults
pytz 2018.7 py36_0 defaults
pywavelets 1.0.1 py36h1d22016_0 defaults
pyyaml 3.13 py36h1de35cc_0 defaults
pyzmq 17.1.2 py36h1de35cc_0 defaults
qt 5.9.6 h45cd832_2 defaults
qtawesome 0.5.2 py36_0 defaults
qtconsole 4.4.2 py36_0 defaults
qtpy 1.5.2 py36_0 defaults
readline 7.0 h1de35cc_5 defaults
requests 2.20.0 py36_0 defaults
rope 0.11.0 py36_0 defaults
ruamel_yaml 0.15.46 py36h1de35cc_0 defaults
scikit-image 0.14.0 py36h0a44026_1 defaults
scikit-learn 0.20.0 py36h4f467ca_1 defaults
scipy 1.1.0 py36h28f7352_1 defaults
seaborn 0.9.0 py36_0 defaults
send2trash 1.5.0 py36_0 defaults
service_identity 17.0.0 py36h28b3542_0 defaults
setuptools 40.5.0 py36_0 defaults
simplegeneric 0.8.1 py36_2 defaults
singledispatch 3.4.0.3 py36hf20db9d_0 defaults
sip 4.19.8 py36h0a44026_0 defaults
six 1.11.0 py36_1 defaults
snappy 1.1.7 he62c110_3 defaults
snowballstemmer 1.2.1 py36h6c7b616_0 defaults
sortedcollections 1.0.1 py36_0 defaults
sortedcontainers 2.0.5 py36_0 defaults
sphinx 1.8.1 py36_0 defaults
sphinxcontrib 1.0 py36_1 defaults
sphinxcontrib-websupport 1.1.0 py36_1 defaults
spyder 3.3.1 py36_1 defaults
spyder-kernels 0.2.6 py36_0 defaults
sqlalchemy 1.2.13 py36h1de35cc_0 defaults
sqlite 3.24.0 ha441bb4_0 defaults
statsmodels 0.9.0 py36h1d22016_0 defaults
sympy 1.3 py36_0 defaults
tblib 1.3.2 py36hda67792_0 defaults
terminado 0.8.1 py36_1 defaults
testpath 0.4.2 py36_0 defaults
tk 8.6.8 ha441bb4_0 defaults
toolz 0.9.0 py36_0 defaults
tornado 5.1.1 py36h1de35cc_0 defaults
tqdm 4.28.1 py36h28b3542_0 defaults
traitlets 4.3.2 py36h65bd3ce_0 defaults
twisted 17.5.0 py36_0 defaults
typed-ast 1.1.0 py36h1de35cc_0 defaults
unicodecsv 0.14.1 py36he531d66_0 defaults
unixodbc 2.3.7 h1de35cc_0 defaults
urllib3 1.23 py36_0 defaults
virtualenv 16.1.0 <pip>
wcwidth 0.1.7 py36h8c6ec74_0 defaults
webencodings 0.5.1 py36_1 defaults
werkzeug 0.14.1 py36_0 defaults
wheel 0.32.2 py36_0 defaults
widgetsnbextension 3.4.2 py36_0 defaults
wrapt 1.10.11 py36h1de35cc_2 defaults
xlrd 1.1.0 py36_1 defaults
xlsxwriter 1.1.2 py36_0 defaults
xlwings 0.14.0 py36_0 defaults
xlwt 1.2.0 py36h5ad1178_0 defaults
xz 5.2.4 h1de35cc_4 defaults
yaml 0.1.7 hc338f04_2 defaults
zeromq 4.2.5 h0a44026_1 defaults
zict 0.1.3 py36_0 defaults
zlib 1.2.11 hf3cbc9b_2 defaults
zope 1.0 py36_1 defaults
zope.interface 4.6.0 py36h1de35cc_0 defaults
zstd 1.3.3 h2a6be3a_0 defaults
mjspeck
All 59 comments
Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh
conda activate my_env
Closing as non-issue. Feel free to re-open if you feel otherwise.
* EDIT *
In the commands above, replace ~/anaconda3/ with the path to your miniconda / anaconda installation. You can find that out by running: conda info | grep -i 'base environment'
nehaljwani
on 24 Nov 2018
@nehaljwani How would you do this, for example, in a makefile, and is there a simple way to get the path to conda.sh programmatically (say from the name of the environment or an environment.yml file)?
mforbes
on 23 Feb 2019
That seems a messy solution to the issue. Now there is a source line in your bash scripts that has to explicitly reference your conda installation path, making them not very portable.
If you use something like source $CONDA_PREFIX/etc/profile.d/conda.sh to get around this, it then makes the script error in everything but the base environment. You could comment in your script that it can only be run from the base, but again: messy.
Is there a conda variable that always returns your base path regardless of your current location?
rbutleriii
on 13 Mar 2019
@rbutleriii
Is there a conda variable that always returns your base path regardless of your current location?
Try this:
CONDA_BASE=$(conda info --base)
stuarteberg
on 14 Mar 2019
@nehaljwani When conda is installed and a user's .bashrc is modified, should the following lines be added to .bashrc? That might save the users some headache. It enables conda to be called from bash scripts without sourcing $(conda info --base)/etc/profile.d/conda.sh.
export -f conda
export -f __conda_activate
export -f __conda_reactivate
export -f __conda_hashr
Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh conda activate my_envClosing as non-issue. Feel free to re-open if you feel otherwise.
that works perfectly~!!!
shenweihai1
on 17 Apr 2019
I'm trying that, but get:
➜ /Users/michael source ~/miniconda3/etc/profile.d/conda.sh
/Users/michael/miniconda3/etc/profile.d/conda.sh:30: parse error near `}'
I'm on Mojave and installed with Miniconda3-latest-MacOSX-x86_64.pkg
kagemusha
on 8 May 2019
This is not a non-issue @nehaljwani. As a user, I would expect that when I run "conda init", that it would prepare my shell for use of "conda activate" everywhere, including within scripts. But it doesn't.
The expected behavior should be exactly what @mjspeck specified, namely that "conda should activate in a bash script the same way it does on the command line".
@rbutleriii is correct that your proposal of adding the line ~/$MY_CONDA_INSTALLATION/etc/profile.d/conda.sh before calling "conda activate" now directly references your personal conda installation. That means that tools that generate "conda activate" calls (e.g. Nextflow) would have to be hand-patched for them to work correctly.
@stuarteberg proposed a perfectly reasonable solution that works (I tested it and yes it works), namely that conda init could add the following to your ~/.bashrc:
export -f conda
export -f __conda_activate
export -f __conda_reactivate
export -f __conda_hashr
I respectfully ask that you re-open this issue and use @stuarteberg's solution (or some other solution) fulfill the expected behavior requested by @mjspeck (i.e. "conda should activate in a bash script the same way it does on the command line"), because that behavior is (I believe) what conda's users are expecting. @stuarteberg's solution would be very easy to implement, and would indeed drastically reduce headaches.
Thank you!!
jasonsydes
on 14 May 2019
@jasonsydes I fully agree.
I also had to add export -f __add_sys_prefix_to_path to my .bashrc in order to get rid of the __add_sys_prefix_to_path: command not found error.
Also note that, until this get fixed, you need to keep these export statements outside of the # >>> conda initialize >>> block so that it doesn't get removed in case you later run conda init bash
pheidippides
on 15 May 2019
+1 for re-opening
stuarteberg
on 15 May 2019
I have noticed that you can do:
eval "$(conda shell.bash hook)"
conda activate <env-name>
scopatz
on 15 May 2019
Happy to reopen this, but we have no intention of doing development on this any time soon. The shell scripts are devilishly complicated, and we don't have time to get into them right now. What looks like a "simple change" may break a terrible number of seemingly unrelated stuff.
Community PRs are most welcome.
msarahan
on 15 May 2019
@mjspeck
for Windows:
- Install Git Bash
- Open Git Bash
- type
source ~/anaconda3/etc/profile.d/conda.sh - type
conda init - Restart your shell
- Profit.
FlamesoFF
on 29 Jul 2019
@mjspeck
for Windows:
- Install Git Bash
- Open Git Bash
- type
source ~/anaconda3/etc/profile.d/conda.sh- type
conda init- Restart your shell
- Profit.
this works
Nilanshrajput
on 2 Aug 2019
This fixed the issue in my makefile: https://stackoverflow.com/a/55696820/4279266
andrew-schweitzer-analog
on 7 Aug 2019
I think a cleaner way is:
eval "$(conda shell.bash hook)"
conda activate my_env
bryant1410
on 23 Aug 2019
On the windows environment use "anaconda prompt" instead of "command prompt".
Go to search.
Type "anaconda prompt" and open it.
Then type "conda activate
SmadusankaB
on 23 Aug 2019
Happy to reopen this, but we have no intention of doing development on this any time soon. The shell scripts are devilishly complicated, and we don't have time to get into them right now. What looks like a "simple change" may break a terrible number of seemingly unrelated stuff.
Community PRs are most welcome.
If you don't trust the project testing enough for doing delicate changes, how can you trust community PRs doing delicate changes?
omry
on 26 Aug 2019
It almost feels automation-hostile... for now this seems to work:
echo "export -f conda" >> "$HOME/.bashrc"
echo "export -f __conda_activate" >> "$HOME/.bashrc"
echo "export -f __conda_reactivate" >> "$HOME/.bashrc"
echo "export -f __conda_hashr" >> "$HOME/.bashrc"
echo "export -f __add_sys_prefix_to_path" >> "$HOME/.bashrc"
echo 'eval "$(conda shell.bash hook)"' >> "$HOME/.bashrc"
I wonder how long before I run into the next issue....
EDIT: Well, in some cases it does, in others it doesn't. In the latter cases it seems to help to explicitly execute eval "$(conda shell.bash hook)" at the beginning of the script, even though it already ran when .bashrc was sourced...
Toxyl
on 18 Sep 2019
For those wanting to work around the above suggestions, source activate likely has the expected behavior, and hopefully one day conda activate will work as expected too. (We felt uncomfortable adding any of the above suggestions into a maintained codebase.)
lmeyerov
on 30 Sep 2019
Another solution is to call your script with bash -i to invoke your interactive environment.
@scopatz -- I just learned that little trick as well. Do you have any idea what it does?
abalter
on 6 Nov 2019
@abalter - yeah it basically builds the activation script in $(conda shell.bash hook) and then runs it in the current interpreter session (eval), which allows conda activate <env-name> to work.
scopatz
on 7 Nov 2019
@abalter
The -i option starts bash in interactive mode that means that it loads your ~/.bashrc file, and you probably have conda activation there.
technic
on 8 Nov 2019
Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh conda activate my_envClosing as non-issue. Feel free to re-open if you feel otherwise.
Works perfect for me :) Thanks a ton.
PallawiSinghal
on 20 Nov 2019
most cleaner option will be
eval "$(conda shell.bash hook)"
conda activate my_env
cervantes-loves-ai
on 26 Nov 2019
@abalter
The-ioption startsbashin interactive mode that means that it loads your~/.bashrcfile, and you probably have conda activation there.
This gets to another question and the reason I was looking at this issue. On linux systems, why is ~/.bashrc modified rather than ~/.bash_profile? A non-interactive shell will not normally source ~/.bashrc.
What is the recommended method to activate a conda environment from a non-interactive shell?
DoaneAS
on 27 Nov 2019
This gets to another question and the reason I was looking at this issue. On linux systems, why is
~/.bashrcmodified rather than~/.bash_profile? A non-interactive shell will not normally source~/.bashrc.
In Ubuntu (and in other distributions that I can't remember), by default ~/.bash_profile sources ~/.profile, which in turns sources ~/.bashrc. So ~/.bashrc will be loaded regardless of it's interactive or not.
bryant1410
on 27 Nov 2019
I have noticed that you can do:
eval "$(conda shell.bash hook)" conda activate <env-name>
Helped activating my prod env when building my docker image :)
hzitoun
on 29 Nov 2019
So this is gotten to be a pretty confusing thread.
@msarahan: I understand that this is a complicated process, and conda does not want to add anything to conda without through testing, but for now:
Is there a recommendation for how to automate manipulation of conda environments? My use case at hand is to want to automate start up scripts -- make an environment, add some packages, active it, run an app in it.
It seems there is not recommended way to do that with a shell script.
Would a python script be easier?
Or do we just give up and not try to use conda environments in that way at this point?
Thanks
ChrisBarker-NOAA
on 7 Dec 2019
The eval and then activate option works on direnv too, that basically spawns bash to collect exported variables or execute commands
richerve
on 15 Jan 2020
Adding eval "$(conda shell.bash hook)" to bashrc automatically resolve this issue on startup for Git Bash within Vscode.
Natemen96
on 29 Mar 2020
source ~/anaconda3/etc/profile.d/conda.sh
conda activate my_env
thank you so much
cervantes-loves-ai
on 1 Apr 2020
it doesn't work on cygwin, it has failed with the error message
$ source /cygdrive/c/tools/miniconda/etc/profile.d/conda.sh
$ conda activate base
$ conda env list
: No such file or directoryiconda/Scripts/conda.exe
$
more verbose log output
Click to expand
```
$ source /cygdrive/c/tools/miniconda/etc/profile.d/conda.sh
- source /cygdrive/c/tools/miniconda/etc/profile.d/conda.sh
++ export CONDA_EXE=C:/tools/miniconda/Scripts/conda.exe
++ CONDA_EXE=C:/tools/miniconda/Scripts/conda.exe
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=C:/tools/miniconda/python.exe
++ CONDA_PYTHON_EXE=C:/tools/miniconda/python.exe
++ '[' -z '' ']'
++ export CONDA_SHLVL=0
++ CONDA_SHLVL=0
++ '[' -n x ']'
++ '[' -n x ']'
+++ dirname C:/tools/miniconda/Scripts/conda.exe
++ PATH=C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
++ export PATH
++ '[' -z x ']'
$ conda activate base
- conda activate base
- '[' 2 -lt 1 ']'
- local cmd=activate
- shift
- case "$cmd" in
- __conda_activate activate base
- '[' -n '' ']'
- local cmd=activate
- shift
- local ask_conda
- CONDA_INTERNAL_OLDPATH=C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- __add_sys_prefix_to_path
- '[' -n '' ']'
++ dirname C:/tools/miniconda/Scripts/conda.exe - SYSP=C:/tools/miniconda/Scripts
++ dirname C:/tools/miniconda/Scripts - SYSP=C:/tools/miniconda
- '[' -n x ']'
- PATH=C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- PATH=C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- PATH=C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- PATH=C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- PATH=C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- PATH=C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- export PATH
++ PS1='[\e]0;\w\a]\n[\e[32m]\u@\h [\e[33m]\w[\e[0m]\n\$ '
++ C:/tools/miniconda/Scripts/conda.exe shell.posix activate base - ask_conda='PS1='\''(base) [\e]0;\w\a]\n[\e[32m]\u@\h [\e[33m]\w[\e[0m]\n\$ '\''
export PATH='\''/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin'\''
export CONDA_PREFIX='\''C:\tools\miniconda'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/cygdrive/c/tools/miniconda/Scripts/conda.exe'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
'xport CONDA_PYTHON_EXE='\''/cygdrive/c/tools/miniconda/python.exe'\'' - rc=0
- PATH=C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin
- eval 'PS1='\''(base) [\e]0;\w\a]\n[\e[32m]\u@\h [\e[33m]\w[\e[0m]\n\$ '\''
export PATH='\''/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin'\''
export CONDA_PREFIX='\''C:\tools\miniconda'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/cygdrive/c/tools/miniconda/Scripts/conda.exe'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
'xport CONDA_PYTHON_EXE='\''/cygdrive/c/tools/miniconda/python.exe'\''
'+ PS1='(base) [\e]0;\w\a]\n[\e[32m]\u@\h [\e[33m]\w[\e[0m]\n\$
++ export $'PATH=/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
++ PATH=$'/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
'+ export 'CONDA_PREFIX=C:\tools\miniconda
'+ CONDA_PREFIX='C:\tools\miniconda
++ export $'CONDA_SHLVL=1\r'
++ CONDA_SHLVL=$'1\r'
++ export $'CONDA_DEFAULT_ENV=base\r'
++ CONDA_DEFAULT_ENV=$'base\r'
'+ export 'CONDA_PROMPT_MODIFIER=(base)
'+ CONDA_PROMPT_MODIFIER='(base)
++ export $'CONDA_EXE=/cygdrive/c/tools/miniconda/Scripts/conda.exe\r'
++ CONDA_EXE=$'/cygdrive/c/tools/miniconda/Scripts/conda.exe\r'
++ export $'_CE_M=\r'
++ _CE_M=$'\r'
++ export $'_CE_CONDA=\r'
++ _CE_CONDA=$'\r'
++ export $'CONDA_PYTHON_EXE=/cygdrive/c/tools/miniconda/python.exe\r'
++ CONDA_PYTHON_EXE=$'/cygdrive/c/tools/miniconda/python.exe\r' - '[' 0 '!=' 0 ']'
- __conda_hashr
- '[' -n '' ']'
- '[' -n '' ']'
- hash -r
(base)
conda env list - conda env list
- '[' 2 -lt 1 ']'
- local cmd=env
- shift
- case "$cmd" in
- CONDA_INTERNAL_OLDPATH=$'/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- __add_sys_prefix_to_path
- '[' -n $'\r' ']'
- '[' -n x ']'
++ dirname $'/cygdrive/c/tools/miniconda/Scripts/conda.exe\r'
bash: dirname: command not found - SYSP=
- '[' -n x ']'
- PATH=$'/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- PATH=$'/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- PATH=$'/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- PATH=$'/Library/usr/bin:/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- PATH=$'/Library/mingw-w64/bin:/Library/usr/bin:/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- PATH=$':/Library/mingw-w64/bin:/Library/usr/bin:/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- export PATH
- $'/cygdrive/c/tools/miniconda/Scripts/conda.exe\r' $'\r' $'\r' env list
: No such file or directoryiconda/Scripts/conda.exe - local t1=127
- PATH=$'/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r'
- return 127
(base)
```
for some reason conda init bash doesn't respect line-feeds, converting them to CRLF, then in conda.sh we see CRs or '\r', also CONDA_PREFIX returned as Windows-native path
$ /cygdrive/c/tools/miniconda/Scripts/conda.exe shell.posix activate base
+ /cygdrive/c/tools/miniconda/Scripts/conda.exe shell.posix activate base
PS1='(base) \[\033[1;36m\]18:50:35\[\e[0m\] \[\033[1;34m\]\w\[\e[0m\] \[\033[1;31m\]$\[\e[0m\] '
export PATH='/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/too
ls/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:/cygdrive/c/tools/miniconda/condabin:/usr/local/bin:/usr/
bin'
export CONDA_PREFIX='C:\tools\miniconda'
export CONDA_SHLVL='1'
export CONDA_DEFAULT_ENV='base'
export CONDA_PROMPT_MODIFIER='(base) '
export CONDA_EXE='/cygdrive/c/tools/miniconda/Scripts/conda.exe'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/cygdrive/c/tools/miniconda/python.exe'
avoidik
on 1 Apr 2020
We do not support Cygwin yet. PRs welcome. The only Unix shells we support at present are the MSYS2 shell and Git for Windows.
mingwandroid
on 2 Apr 2020
I have stumpled across this problem a few days ago, too. Apparently, conda is not fully/properly initialised for non-interactive shell sessions/environments.
I am using bash, and have set up a JupyterLab with conda in my home directory doing
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3
${HOME}/miniconda3/bin/conda init bash
${HOME}/miniconda3/bin/conda config --set auto_activate_base false
${HOME}/miniconda3/bin/conda install -n base jupyterlab
If I do in a fresh bash login session (on an HPC system, but that is not really important here)
conda activate base && jupyter lab --ip=$(hostname) --no-browser
then everything works as expected. If I set up a bash script that contains
#!/bin/bash
conda activate base && jupyter lab --ip=$(hostname) --no-browser
and that I execute with
./jupyterlab.sh
I get the following error
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
[...]
As my .bashrc already contains the necessary conda initialisation part, I tried to investigate the problem a little bit deeper, and have found my script to work if I explicitely set an interactive bash environment by using the interactive flag in the header
#!/bin/bash -i
conda activate base && jupyter lab --ip=$(hostname) --no-browser
In the end, however, I have decided to go with
#!/usr/bin/env bash
eval "$(conda shell.bash hook)" # properly initialise non-interactive shell
conda activate base && \
jupyter lab --ip=$(hostname) --no-browser
which also works as expected.
I don't really know, if this is of any help here. But I wanted to leave a quick note about the aspect of interactive vs. non-interactive shell sessions/environments, that has not yet explicitely been mentioned above.
(For completion, I have Ubuntu 18.04.4 LTS with bash 4.4.20 and conda 4.8.3.)
kathoef
on 5 May 2020
@kathoef
Somebody decided in the name of efficiency (?) to place the following code in the default .bashrc
# If not running interactively, don't do anything
case $- in
*i*) ;;
*) return;;
esac
Conda initialisation code is inserted at the end of .bashrc. So, the sourcing terminates before the conda initialisation code is reached.
The issue had been bugging me for over a year until I decided to review .bashrc line by line from the beginning and discovered the culprit.
For portability, I currently use the following code:
if [[ -n "$CONDA_EXE" ]]; then
condaSetup="$($CONDA_EXE 'shell.bash' 'hook' 2> /dev/null)"
eval "$condaSetup"
else
if [[ -n "$CONDA_PREFIX" ]]; then
source ${CONDA_PREFIX%/envs/*}/etc/profile.d/conda.sh
else
echo "Unable to initialise conda function. Please check if CONDA variables are exported."
fi
fi
That works fine as long as you init conda in .bashrc and your job scheduling system passes the environmental variables on.
brisk022
on 5 May 2020
if you'd run a terminal interactively it should work just fine, for example in ubuntu and friends this option usually disabled by default
avoidik
on 5 May 2020
you may solve cygwin issue on Windows by creating a new global environment variable SHELLOPTS=igncr and setting relevant paths manually
avoidik
on 5 May 2020
source ~/anaconda3/etc/profile.d/conda.sh
conda activate@nehaljwani, thanks, much, works perfectly
@lboy27282 you should add "works perfectly _on your machine_". And this is why nehaljwani's answer was downvoted so much.
Try porting your script to a prod environment where conda installation path might be different and you'll see what I mean.
JivanRoquet
on 11 Jul 2020
I've created a conda environment as well as added the path in Google Colab
import sys
_ = (sys.path
.append("/usr/local/lib/python3.6/site-packages"))
But while activating the environment, It throws the following error.
Also tried as suggested earlier, but I'm not sure where the profile.d/conda.sh is located in my colab notebook.
I'm not sure what is it related to. I know its tricky to work with Google Colab but I'm hoping to get some help here. Thanks.
Also,
the environment is successfully listed in the condo env list as below.
Thanks for finding some time for this. I hope it's resolvable in due time.
cs145442
on 15 Jul 2020
I know nothing of Google Colab, but:
sys.path .append("/usr/local/lib/python3.6/site-packages")
Is a Bad Idea -- you really don't want to mix system with conda environments. It's kind of the point to NOT use usr/local -- that's why you have conda.
ChrisBarker-NOAA
on 15 Jul 2020
you should add "works perfectly _on your machine_". And this is why nehaljwani's answer was downvoted so much.
@JivanRoquet You're not being fair. Why don't you say @nehaljwani's answer was upvoted so much? Before this issue is officially fixed (which is surprising that we're already in 2020 and it still is not!), it is the easiest solution to try first.
leofang
on 15 Jul 2020
@mjspeck
for Windows:
- Install Git Bash
- Open Git Bash
- type
source ~/anaconda3/etc/profile.d/conda.sh- type
conda init- Restart your shell
- Profit.
and in sh:
I think a cleaner way is:
eval "$(conda shell.bash hook)" conda activate my_env
this works
iterateself
on 3 Aug 2020
@mjspeck
for Windows:
- Install Git Bash
- Open Git Bash
- type
source ~/anaconda3/etc/profile.d/conda.sh- type
conda init- Restart your shell
- Profit.
Any idea how to undo this? Now whenever I open Git bash, it automatically activates the base Conda environment.
osharaki
on 8 Aug 2020
open bash profile file and remove lines added by conda, restart terminal
windows
avoidik
on 8 Aug 2020
open bash profile file and remove lines added by conda, restart terminal windows
Thank you, this works. Is there a way to achieve the same effect without having Conda activate automatically every time?
As a side note, it seems conda init disabled the password prompt (SSH agent) that I usually get when opening a new git bash terminal. Can't seem to get it back.
osharaki
on 8 Aug 2020
you may try to disable base env activation by setting configuration
parameter:
conda config --set auto_activate_base false
or add this line before init script
export CONDA_AUTO_ACTIVATE_BASE="false"
avoidik
on 8 Aug 2020
you may try to disable base env activation by setting configuration parameter: conda config --set auto_activate_base false or add this line before init script export CONDA_AUTO_ACTIVATE_BASE="false"
Where can I find the init script?
osharaki
on 8 Aug 2020
the lines added by conda to your bash profile file is init script
avoidik
on 8 Aug 2020
@mjspeck
for Windows:
- Install Git Bash
- Open Git Bash
- type
source ~/anaconda3/etc/profile.d/conda.sh- type
conda init- Restart your shell
- Profit.
For anyone else trying this, this only worked for me when I typed conda init bash in step 4. However, if you're using an SSH agent, this will prevent the password prompt from appearing.
osharaki
on 8 Aug 2020
conda init knows how to update the ~/.bashrc so that conda is properly initialized in the interactive bash environment.
It updates what appears inside
# >>> conda initialize >>>
...
# <<< conda initialize <<<
Would it be unreasonable to ask that conda init take a file name (presumably a bash script) containing the requisite delimiters and update that script?
phreed
on 19 Aug 2020
@mjspeck
for Windows:
- Install Git Bash
- Open Git Bash
- type
source ~/anaconda3/etc/profile.d/conda.sh- type
conda init- Restart your shell
- Profit.
How do i restart my shell?
hwtrost
on 6 Sep 2020
@hwtrost
How do i restart my shell?
Close and open again your terminal window / tab ;)
technic
on 6 Sep 2020
Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh conda activate my_envClosing as non-issue. Feel free to re-open if you feel otherwise.
* EDIT *
In the commands above, replace~/anaconda3/with the path to your miniconda / anaconda installation. You can find that out by running:conda info | grep -i 'base environment'
What if I am using an ssh? when I do conda info, it just gives me a directory for where the environment is installed in the cluster, not a sh file.
Hanxi-001
on 25 Sep 2020
Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh conda activate my_envClosing as non-issue. Feel free to re-open if you feel otherwise.
* EDIT *
In the commands above, replace~/anaconda3/with the path to your miniconda / anaconda installation. You can find that out by running:conda info | grep -i 'base environment'
Thanks! Very helpful for me.
manliu1225
on 5 Oct 2020
In my case it is because WSL bash doesn't load .bashrc but it loads .bash_profile, so I add lines
if [[ -f ~/.bashrc ]] ; then
. ~/.bashrc
fi
to my .bash_profile to load .bashrc
vitaminac
on 11 Nov 2020
@scopatz
eval "$(conda shell.bash hook)"
conda activate
This actually doesn't work for me
Traceback (most recent call last):
File "/home/buechel/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 98, in main
return activator_main()
File "/home/buechel/miniconda3/lib/python3.7/site-packages/conda/activate.py", line 630, in main
activator = Activator(shell, activator_args)
File "/home/buechel/miniconda3/lib/python3.7/site-packages/conda/activate.py", line 136, in __init__
raise NotImplementedError()
NotImplementedError
buechel
on 24 Nov 2020
This works for me:
1- Add this to your .bashrc file in the home repository (_C:/Users/
source <path_to_your_anaconda_installation_folder>/anaconda3/etc/profile.d/conda.sh
2- Restart your shell.
conda activate <env-name> should work now
d2416
on 18 Dec 2020
@nehaljwani When conda is installed and a user's
.bashrcis modified, should the following lines be added to.bashrc? That might save the users some headache. It enables conda to be called from bash scripts without sourcing$(conda info --base)/etc/profile.d/conda.sh.export -f conda export -f __conda_activate export -f __conda_reactivate export -f __conda_hashr
Could you elaborate how could I do this?
ShenTTT
on 21 Jan 2021
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Most helpful comment
Functions are not exported by default to be made available in subshells. I'd recommend you do:
Closing as non-issue. Feel free to re-open if you feel otherwise.
* EDIT *
In the commands above, replace
~/anaconda3/with the path to your miniconda / anaconda installation. You can find that out by running:conda info | grep -i 'base environment'