Can't execute conda activate from bash script #7980
Description
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