Can not access Anaconda/Miniconda environment as virtualenv #178

oscargicast · 2016-06-19T05:17:32Z

I'm showing you the steps I use to create a virtualenv based on miniconda. Finally you will see that the virtualenv was created but I can't access to it.

1.0. Check my initial pyenv versions:

$ pyenv versions
* system (set by /home/oscar/.python-version)
2.7.9
3.5.1

1.1 Install miniconda:

$ pyenv install miniconda3-4.0.5

$ pyenv versions
* system (set by /home/oscar/.python-version)
  2.7.9
  3.5.1
  miniconda3-4.0.5

1.2. Create the venvtest virtualenv based on miniconda:

$ pyenv virtualenv miniconda3-4.0.5 venvtest

$ pyenv versions
* system (set by /home/oscar/.python-version)
  2.7.9
  3.5.1
  miniconda3-4.0.5
  miniconda3-4.0.5/envs/venvtest
  venvtest

When I want to check if the virtualenv was created, It doesn't show it. So I can't no access to it 😢

$ pyenv virtualenvs
  miniconda3-4.0.5 (created from /home/oscar/.pyenv/versions/miniconda3-4.0.5)

$ pyenv activate ... (autocompleting)
--help            miniconda3-4.0.5  --unset

Please, I hope you can help me.

quietcoolwu · 2016-06-25T03:04:47Z

@yyuu The same problem happened to me, but it's still OK when I installed Anaconda or Miniconda with older conda version(e.g. 4.0.5), and using pyenv virtualenv to create a virtualenv. That is to say all works normally with older conda version after pyenv update.
I saw the conda update-log showed that it fixed shell recursion with activate problem in 4.1.3, but when I update to this version the problem remains.

yyuu · 2016-07-05T00:55:47Z

I couldn't reproduce the issue. It's all working for me even with conda 4.1.4.

% conda --version
conda 4.1.4
% pyenv virtualenv anaconda3-4.1.0 foo
Fetching package metadata .......
Solving package specifications: ..........

Package plan for installation in environment /home/yyuu/.pyenv/versions/anaconda3-4.1.0/envs/foo:

The following NEW packages will be INSTALLED:

    openssl:    1.0.2h-1     
    pip:        8.1.2-py35_0 
    python:     3.5.1-5      
    readline:   6.2-2        
    setuptools: 23.0.0-py35_0
    sqlite:     3.13.0-0     
    tk:         8.5.18-0     
    wheel:      0.29.0-py35_0
    xz:         5.2.2-0      
    zlib:       1.2.8-3      

Linking packages ...
[      COMPLETE      ]|###########################################################################################################################################################| 100%
#
# To activate this environment, use:
# $ source activate foo
#
# To deactivate this environment, use:
# $ source deactivate
#
Installing pip from https://bootstrap.pypa.io/get-pip.py...
Requirement already up-to-date: pip in /home/yyuu/.pyenv/versions/anaconda3-4.1.0/envs/foo/lib/python3.5/site-packages
% pyenv virtualenvs
* anaconda3-4.1.0 (created from /home/yyuu/.pyenv/versions/anaconda3-4.1.0)
  anaconda3-4.1.0/envs/foo (created from /home/yyuu/.pyenv/versions/anaconda3-4.1.0/envs/foo)
  foo (created from /home/yyuu/.pyenv/versions/foo)
  miniconda3-4.0.5 (created from /home/yyuu/.pyenv/versions/miniconda3-4.0.5)
% pyenv activate foo
% pyenv virtualenvs
  anaconda3-4.1.0 (created from /home/yyuu/.pyenv/versions/anaconda3-4.1.0)
  anaconda3-4.1.0/envs/foo (created from /home/yyuu/.pyenv/versions/anaconda3-4.1.0/envs/foo)
* foo (created from /home/yyuu/.pyenv/versions/foo)
  miniconda3-4.0.5 (created from /home/yyuu/.pyenv/versions/miniconda3-4.0.5)

TheBurnDoc · 2016-07-13T07:35:31Z

For me, on conda 4.1.2 I had to run source ~/.pyenv/versions/<env_dir>/bin/activate <env_name> at least once to make it work

motivic · 2017-12-30T15:39:36Z

This issue is resurfacing with conda 4.4.1

% pyenv virtualenv miniconda3-latest test
Solving environment: done

## Package Plan ##

  environment location: /home/johnson/.pyenv/versions/miniconda3-latest/envs/test

  added / updated specs: 
    - python


The following NEW packages will be INSTALLED:

    ca-certificates: 2017.08.26-h1d4fec5_0   
    certifi:         2017.11.5-py36hf29ccca_0
    libedit:         3.1-heed3624_0          
    libffi:          3.2.1-hd88cf55_4        
    libgcc-ng:       7.2.0-h7cc24e2_2        
    libstdcxx-ng:    7.2.0-h7a57d05_2        
    ncurses:         6.0-h9df7e31_2          
    openssl:         1.0.2n-hb7f436b_0       
    pip:             9.0.1-py36h6c6f9ce_4    
    python:          3.6.4-hc3d631a_0        
    readline:        7.0-ha6073c6_4          
    setuptools:      36.5.0-py36he42e2e1_0   
    sqlite:          3.20.1-hb898158_2       
    tk:              8.6.7-hc745277_3        
    wheel:           0.30.0-py36hfd4bba0_1   
    xz:              5.2.3-h55aa19d_2        
    zlib:            1.2.11-ha838bed_2       

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate test
#
# To deactivate an active environment, use:
# > source deactivate
#

Requirement already satisfied: setuptools in /home/johnson/.pyenv/versions/miniconda3-latest/envs/test/lib/python3.6/site-packages
Requirement already satisfied: pip in /home/johnson/.pyenv/versions/miniconda3-latest/envs/test/lib/python3.6/site-packages

% pyenv activate test                                                   
pyenv-virtualenv: version `test' is not a virtualenv

Also, conda and activate are both missing from ~/.pyenv/versions/test/bin:

  % ls ~/.pyenv/versions/test/bin                                          !930
2to3              lzgrep            python3.6m         unxz
2to3-3.6          lzless            python3.6m-config  wheel
captoinfo         lzma              python3-config     wish
clear             lzmadec           pyvenv             wish8.6
c_rehash          lzmainfo          pyvenv-3.6         xz
easy_install      lzmore            reset              xzcat
easy_install-3.6  ncursesw6-config  sqlite3            xzcmp
idle3             openssl           sqlite3_analyzer   xzdec
idle3.6           pip               tabs               xzdiff
infocmp           pydoc             tclsh              xzegrep
infotocap         pydoc3            tclsh8.6           xzfgrep
lzcat             pydoc3.6          tic                xzgrep
lzcmp             python            toe                xzless
lzdiff            python3           tput               xzmore
lzegrep           python3.6         tset
lzfgrep           python3.6-config  unlzma

Update: Reverting back to conda 4.3.23 resolved the issue. Seems to be caused by an update in conda 4.4 that changed how conda manages environments.

willprice · 2018-01-08T16:31:46Z

I too am having the same issue describe by @motivic. Reverting back to 4.3.27 fixes the issue for me, was running miniconda3-latest installed this morning (4.4.6)

AdityaGudimella · 2018-01-11T22:49:55Z

@TurboTim 's suggestion still works with conda 4.4.* though.

omdv · 2018-01-22T05:10:13Z

Confirming that I had the described issue with conda-4.4.7, which disappeared after downgrading conda to 4.3.30

gzagatti · 2018-01-30T21:20:40Z

I managed to make it work after downgrading to miniconda3-4.3.27 and downgrading conda within miniconda to the same version. Finally, I made sure to create a new conda environment using pyenv.

vrastogi · 2018-02-21T23:20:06Z

Facing this same issue here with conda 4.4.10. For me there does not appear to be an activate in bin of the env created.

willprice · 2018-02-22T08:36:54Z

conda 4.x switched to using conda activate env-name

vrastogi · 2018-02-22T17:44:55Z

Thanks, the comment by @willprice helps to at least enable the environments with conda. Activate the environment does not work with pyenv activate however.

frankhinek · 2018-02-26T20:18:34Z

I'm having the exact same issue.

@yyuu Are there plans to fix this for versions of conda > 4.4.x?

Moulick · 2018-02-26T23:42:47Z

Yep, Still a big issue

Moulick · 2018-02-26T23:45:47Z

Although the method by @willprice didn't work, the one above by @TurboTim works

For me, on conda 4.1.2 I had to run source ~/.pyenv/versions/<env_dir>/bin/activate <env_name> at least once to make it work

taschini · 2018-03-06T11:04:34Z

Creating by hand the symbolic links within the environment bin directory to the conda and activate that you find in the conda base environment seems to fix the issue.

E.g.,

ln -s  ~/.pyenv/versions/miniconda3-latest/bin/activate ~/.pyenv/versions/miniconda3-latest/envs/test/bin/
ln -s  ~/.pyenv/versions/miniconda3-latest/bin/conda ~/.pyenv/versions/miniconda3-latest/envs/test/bin/

Edit This work-around is no longer necessary after #290.

teake · 2018-03-06T14:29:23Z

Running into this issue as well, though I'm using fish. For the fish shell, you have to either symlink or source <env_dir>/etc/fish/conf.d/conda.fish instead of <env_dir>/etc/profile.d/conda.sh.

clbarnes · 2018-03-13T14:43:53Z

Even with #251 merged I'm still having this issue. I did

pyenv update
pyenv uninstall miniconda2-latest
pyenv uninstall miniconda3-latest

Then in a new terminal

pyenv install miniconda2-latest
pyenv virtualenv miniconda2-latest my-env
pyenv activate my-env

and got pyenv-virtualenv: version 'my-env' is not a virtualenv

When uninstalling miniconda2-latest again, pyenv does check that I want to remove my-env as well.

teake · 2018-03-20T08:02:31Z

#251 fixed activating an environment via conda:

pyenv install miniconda3-latest
pyenv activate miniconda3-latest
conda create --name myenv python
conda activate myenv

But I agree that doing this via pyenv-virtualenv should also work. (Though the above workflow is sufficient for me so I probably won't put in a PR).

vrastogi · 2018-03-20T18:38:21Z

The solution provided by @taschini fixes the problem and you can directly pyenv activate the conda virtual environment.

@taeke:
The problem with the solution you have (which probably already worked with bash) is that you cannot use facilities that pyenv provides, e.g., activating/deactivating an environment on changing directories.

clbarnes · 2018-03-20T19:19:14Z

@taschini 's answer is a workaround, not a solution. This is something pyenv should do internally, so this issue should be reopened until that's the case.

vrastogi · 2018-03-20T19:20:58Z

@clbarnes I agree that pyenv should provide a built-in solution for this and this thread should remain open to continue tracking the issue.

apapanico · 2018-05-09T20:17:53Z

Just to confirm to anyone visiting this thread. @taschini's solution:

alexp@iMac (main@Py3.6.4):~$ pyenv virtualenv miniconda3-4.3.30 test
...
alexp@iMac (main@Py3.6.4):~$ pyenv versions
  system
  3.6.4
  3.6.4/envs/main
  data8
* main (set by /Users/alexp/.python-version)
  miniconda3-4.3.30
  miniconda3-4.3.30/envs/test
  test
alexp@iMac (main@Py3.6.4):~$ pyenv activate test
pyenv-virtualenv: version `test' is not a virtualenv
alexp@iMac (main@Py3.6.4):~$ ln -s /usr/local/var/pyenv/versions/miniconda3-4.3.30/bin/conda /usr/local/var/pyenv/versions/test/bin/
alexp@iMac (main@Py3.6.4):~$ pyenv activate test
pyenv-virtualenv: version `test' is not a virtualenv
alexp@iMac (main@Py3.6.4):~$ ln -s /usr/local/var/pyenv/versions/miniconda3-4.3.30/bin/activate /usr/local/var/pyenv/versions/test/bin/
alexp@iMac (main@Py3.6.4):~$ pyenv activate test
alexp@iMac (test@PyInc.):~$ pyenv deactivate test
alexp@iMac (main@Py3.6.4):~$

It seems that both conda and activate are required.

I created a pyenv-virtualenv hook for this:

alexp@iMac (main@Py3.6.4):~$ pyenv hooks virtualenv
/usr/local/var/pyenv/pyenv.d/virtualenv/venv_hook.bash

# /usr/local/var/pyenv/pyenv.d/virtualenv/venv_hook.bash

after_virtualenv "BASE_VERSION=\"$(echo $VIRTUALENV_NAME | awk -F/ '{print $(NF-2)}')\""
after_virtualenv "VENVNAME=\"$(echo $VIRTUALENV_NAME | awk -F/ '{print $(NF)}')\""
after_virtualenv 'CONDA=${PYENV_ROOT}/versions/${BASE_VERSION}/bin/conda'
after_virtualenv 'ACTIVATE=${PYENV_ROOT}/versions/${BASE_VERSION}/bin/activate'

after_virtualenv 'if [[ $BASE_VERSION = *"conda"* ]]; then echo "...linking conda and activate"; fi'
after_virtualenv 'if [[ $BASE_VERSION = *"conda"* ]]; then ln -s ${CONDA} ${PYENV_ROOT}/versions/${VENVNAME}/bin/; fi'
after_virtualenv 'if [[ $BASE_VERSION = *"conda"* ]]; then ln -s ${ACTIVATE} ${PYENV_ROOT}/versions/${VENVNAME}/bin/; fi'

After the hook is installed:

alexp@iMac (main@Py3.6.4):~$ pyenv install miniconda3-4.3.30 
Installing Miniconda3-4.3.30.1-MacOSX-x86_64...
...
Installed Miniconda3-4.3.30.1-MacOSX-x86_64 to /usr/local/var/pyenv/versions/miniconda3-4.3.30

alexp@iMac (main@Py3.6.4):~$ pyenv versions
  system
  3.6.4
  3.6.4/envs/main
  data8
* main (set by /Users/alexp/.python-version)
  miniconda3-4.3.30
alexp@iMac (main@Py3.6.4):~$ pyenv virtualenv miniconda3-4.3.30 test
...
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate test
#
# To deactivate an active environment, use:
# > source deactivate
#

Requirement already satisfied: setuptools in /usr/local/var/pyenv/versions/miniconda3-4.3.30/envs/test/lib/python3.6/site-packages
Requirement already satisfied: pip in /usr/local/var/pyenv/versions/miniconda3-4.3.30/envs/test/lib/python3.6/site-packages
...linking conda and activate
alexp@iMac (main@Py3.6.4):~$ pyenv activate test
alexp@iMac (test@PyInc.):~$ pyenv which python
/usr/local/var/pyenv/versions/test/bin/python
alexp@iMac (test@PyInc.):~$ pyenv deactivate test
alexp@iMac (main@Py3.6.4):~$

kondongx · 2018-10-30T09:29:40Z

Creating by hand the symbolic links within the environment bin directory to the conda and activate that you find in the conda base environment seems to fix the issue.

E.g.,
ln -s  ~/.pyenv/versions/miniconda3-latest/bin/activate ~/.pyenv/versions/miniconda3-latest/envs/test/bin/
ln -s  ~/.pyenv/versions/miniconda3-latest/bin/conda ~/.pyenv/versions/miniconda3-latest/envs/test/bin/

fix my problem!

feluxe · 2018-11-11T00:18:40Z

I'm having the same issue. The hook doesn't work on my linux machine.

apapanico · 2018-11-11T01:30:31Z

Did linking work? Or is just the hook? I've found the hooks a bit tricky to program.

kondongx · 2018-11-22T01:53:14Z

Try downgrade miniconda to version-4.3.30:

pyenv activate miniconda3-latest
conda install conda=4.3.30

You can find it from #246.

taschini · 2018-11-26T11:11:57Z

#290 Solved my problem.

jxxiao · 2018-12-14T06:11:09Z

@taschini 's answer is a workaround, not a solution. This is something pyenv should do internally, so this issue should be reopened until that's the case.

Even with #251 merged I'm still having this issue. I did
pyenv update
pyenv uninstall miniconda2-latest
pyenv uninstall miniconda3-latest
Then in a new terminal
pyenv install miniconda2-latest
pyenv virtualenv miniconda2-latest my-env
pyenv activate my-env
and got pyenv-virtualenv: version 'my-env' is not a virtualenv

When uninstalling miniconda2-latest again, pyenv does check that I want to remove my-env as well.

I got the same problem with you. I just confused why I can't activate a miniconda-virtualenv by pyenv activate.I hava to use conda activate.I found #290 It doesn't solve my problem.

jimmywan · 2019-02-19T21:47:39Z

@jxxiao #290 appears towork for me. I don't run pyenv activate, I used pyenv local and/or pyenv shell and they worked fine for me.

In fact, I never even use pyenv activate anymore. Doesn't seem to serve a useful purpose as an end user anymore.

g6ai · 2021-05-25T16:11:22Z

I'm using pyenv 2.0.0 on macOS 10.14.6. pyenv local still does not work for me out-of-box. To be exact, both conda and activate commands are not in the bin directory in env created by miniconda.

yyuu added conda unconfirmed labels Jun 23, 2016

yyuu mentioned this issue Jul 5, 2016

It seems that conda version 4.x breaks pyenv support. pyenv/pyenv#635

Closed

yyuu closed this as completed Jul 5, 2016

willprice mentioned this issue Jan 9, 2018

Conda 4.4.4 breaks pyenv virtual environments #246

Open

teake mentioned this issue Mar 8, 2018

Source conda 4.4.4 shell files #251

Merged

bossjones mentioned this issue Oct 27, 2018

Is there a way to set environment variables for each version? #263

Open

lmmarsano mentioned this issue Nov 21, 2018

Fix: support newer conda #290

Merged

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Can not access Anaconda/Miniconda environment as virtualenv #178

Can not access Anaconda/Miniconda environment as virtualenv #178

oscargicast commented Jun 19, 2016 •

edited by yyuu

quietcoolwu commented Jun 25, 2016 •

edited

yyuu commented Jul 5, 2016

TheBurnDoc commented Jul 13, 2016 •

edited

motivic commented Dec 30, 2017 •

edited

willprice commented Jan 8, 2018

AdityaGudimella commented Jan 11, 2018

omdv commented Jan 22, 2018

gzagatti commented Jan 30, 2018

vrastogi commented Feb 21, 2018

willprice commented Feb 22, 2018

vrastogi commented Feb 22, 2018

frankhinek commented Feb 26, 2018

Moulick commented Feb 26, 2018

Moulick commented Feb 26, 2018

taschini commented Mar 6, 2018 •

edited

teake commented Mar 6, 2018

clbarnes commented Mar 13, 2018 •

edited

teake commented Mar 20, 2018

vrastogi commented Mar 20, 2018

clbarnes commented Mar 20, 2018

vrastogi commented Mar 20, 2018

apapanico commented May 9, 2018 •

edited

kondongx commented Oct 30, 2018

feluxe commented Nov 11, 2018

apapanico commented Nov 11, 2018

kondongx commented Nov 22, 2018

taschini commented Nov 26, 2018

jxxiao commented Dec 14, 2018

jimmywan commented Feb 19, 2019

g6ai commented May 25, 2021 •

edited

Can not access Anaconda/Miniconda environment as virtualenv #178

Can not access Anaconda/Miniconda environment as virtualenv #178

Comments

oscargicast commented Jun 19, 2016 • edited by yyuu

quietcoolwu commented Jun 25, 2016 • edited

yyuu commented Jul 5, 2016

TheBurnDoc commented Jul 13, 2016 • edited

motivic commented Dec 30, 2017 • edited

willprice commented Jan 8, 2018

AdityaGudimella commented Jan 11, 2018

omdv commented Jan 22, 2018

gzagatti commented Jan 30, 2018

vrastogi commented Feb 21, 2018

willprice commented Feb 22, 2018

vrastogi commented Feb 22, 2018

frankhinek commented Feb 26, 2018

Moulick commented Feb 26, 2018

Moulick commented Feb 26, 2018

taschini commented Mar 6, 2018 • edited

teake commented Mar 6, 2018

clbarnes commented Mar 13, 2018 • edited

teake commented Mar 20, 2018

vrastogi commented Mar 20, 2018

clbarnes commented Mar 20, 2018

vrastogi commented Mar 20, 2018

apapanico commented May 9, 2018 • edited

kondongx commented Oct 30, 2018

feluxe commented Nov 11, 2018

apapanico commented Nov 11, 2018

kondongx commented Nov 22, 2018

taschini commented Nov 26, 2018

jxxiao commented Dec 14, 2018

jimmywan commented Feb 19, 2019

g6ai commented May 25, 2021 • edited

oscargicast commented Jun 19, 2016 •

edited by yyuu

quietcoolwu commented Jun 25, 2016 •

edited

TheBurnDoc commented Jul 13, 2016 •

edited

motivic commented Dec 30, 2017 •

edited

taschini commented Mar 6, 2018 •

edited

clbarnes commented Mar 13, 2018 •

edited

apapanico commented May 9, 2018 •

edited

g6ai commented May 25, 2021 •

edited