Conda installation in a Python 3 environment doesn't work #1446

khinsen · 2017-06-29T14:24:07Z

Expected behaviour

conda install mdanalysis should create a working installation of MDAnalysis, or else report an error.

Actual behaviour

When run in a Python 3 conda environment, conda install mdanalysis installs a Python 2 version of MDAnalysis (under lib/python2.7). It does not install Python 2, so the installation is unusable.

Note that the installation instructions nowhere mention if MDAnalysis expects Python 2 or Python 3, so it is certainly not unreasonable to try a conda installation for Python 3.

The text was updated successfully, but these errors were encountered:

kain88-de · 2017-06-29T14:46:04Z

@khinsen we don't have python 3 packages right now. In fact MDAnalysis only has experimental python 3 support right now. We are working on getting full python 3 support this summer.

Until then you have to install MDAnalysis from pip on python3. But be warned that some things might not work.

I'm a bit surprised though that conda just installed the python2 package. Did you install from the conda-forge channel?

khinsen · 2017-06-29T16:43:16Z

Yes. I understand that MDAnalysis has incomplete Python 3 support for now (although it takes a while to figure this out). And then it makes sense not to have a Python 3 conda package. But then I expect one of (1) an error message or (2) an automatic installation of Python 2 as a dependency, with a preference for (1).

kain88-de · 2017-06-29T16:52:59Z

Did you install MDAnalysis from the conda-forge channel?

kain88-de · 2017-06-29T16:54:49Z

What does conda config --show return for you?

orbeckst · 2017-06-29T23:33:53Z

I can confirm: In an anaconda3 environment, conda will happily install a non-functional MDAnalysis.

Package plan for installation in environment /Users/oliver/anaconda3:

The following NEW packages will be INSTALLED:

    biopython:       1.68-np112py35_0
    griddataformats: 0.3.3-py35_0      conda-forge
    hdf4:            4.2.12-0          conda-forge
    joblib:          0.11-py35_0       conda-forge
    libnetcdf:       4.4.1.1-4         conda-forge
    mdanalysis:      0.16.2-np112_0    conda-forge
    mmtf-python:     1.0.7-py35_0      conda-forge
    netcdf4:         1.2.8-np112py35_0 conda-forge

However, despite it being installed by conda, it is not importable

Python 3.5.3 |Anaconda 4.4.0 (x86_64)| (default, Mar  6 2017, 12:15:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import MDAnalysis
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named 'MDAnalysis'
>>>

and as originally reported, it was installed in anaconda3/lib/python2.7/site-packages/

ls anaconda3/lib/python2.7/site-packages/
MDAnalysis                       MDAnalysis-0.16.2-py2.7.egg-info

@kain88-de , this is my config:

conda config --show

gives

add_anaconda_token: True
add_pip_as_python_dependency: True
allow_non_channel_urls: True
allow_softlinks: True
always_copy: False
always_softlink: False
always_yes: False
anaconda_upload: None
auto_update_conda: True
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
  - conda-forge
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
create_default_packages: []
custom_channels:
  pkgs/r: https://repo.continuum.io/
  pkgs/free: https://repo.continuum.io/
  pkgs/pro: https://repo.continuum.io/
custom_multichannels:
  local: []
  defaults: ["https://repo.continuum.io/pkgs/free", "https://repo.continuum.io/pkgs/r", "https://repo.continuum.io/pkgs/pro"]
default_channels:
  - https://repo.continuum.io/pkgs/free
  - https://repo.continuum.io/pkgs/r
  - https://repo.continuum.io/pkgs/pro
disallow: []
envs_dirs:
  - /Users/oliver/anaconda3/envs
  - /Users/oliver/.conda/envs
force: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
offline: False
path_conflict: clobber
pinned_packages: []
pkgs_dirs:
  - /Users/oliver/anaconda3/pkgs
  - /Users/oliver/.conda/pkgs
proxy_servers: {}
quiet: False
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
rollback_enabled: True
shortcuts: True
show_channel_urls: None
ssl_verify: True
track_features: []
use_pip: True
verbosity: 0

orbeckst · 2017-06-29T23:36:30Z

P.S.: I followed our quick-install instructions

conda config --add channels conda-forge
conda install mdanalysis

and the sources

conda config --show-sources
==> /Users/oliver/.condarc <==
channels:
  - conda-forge
  - defaults

khinsen · 2017-06-30T06:53:33Z

Here is my conda configuration:

(root) ~/ $ conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
allow_non_channel_urls: True
allow_softlinks: True
always_copy: False
always_softlink: False
always_yes: False
anaconda_upload: None
auto_update_conda: True
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
  - conda-forge
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
create_default_packages: []
custom_channels:
  pkgs/r: https://repo.continuum.io/
  pkgs/free: https://repo.continuum.io/
  pkgs/pro: https://repo.continuum.io/
custom_multichannels:
  defaults: ["https://repo.continuum.io/pkgs/free", "https://repo.continuum.io/pkgs/r", "https://repo.continuum.io/pkgs/pro"]
  local: []
default_channels:
  - https://repo.continuum.io/pkgs/free
  - https://repo.continuum.io/pkgs/r
  - https://repo.continuum.io/pkgs/pro
disallow: []
envs_dirs:
  - /Users/hinsen/anaconda3/envs
  - /Users/hinsen/.conda/envs
force: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
offline: False
path_conflict: clobber
pinned_packages: []
pkgs_dirs:
  - /Users/hinsen/anaconda3/pkgs
  - /Users/hinsen/.conda/pkgs
proxy_servers: {}
quiet: False
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
rollback_enabled: True
shortcuts: True
show_channel_urls: None
ssl_verify: True
track_features: []
use_pip: True
verbosity: 0

kain88-de · 2017-07-18T15:55:01Z

The conda packages are now not installable on python 3 anymore

goanpeca · 2019-03-11T13:08:26Z

This seems to be still a problem for packages on conda-forge.

Any way I can help?

Cheers

orbeckst · 2019-05-29T23:00:47Z

@goanpeca can you check which version of the conda package gets installed? EDIT: ... and where?

@kain88-de had fixed the problem conda-forge/mdanalysis-feedstock#4 (comment) but I actually don't remember how (probably conda-forge/mdanalysis-feedstock@3b8efbb); we now certainly have the python run time dependency which – to my limited understanding – should ensure that only matching versions of Python should be installed.

goanpeca · 2019-05-29T23:16:12Z

I will check this next week ;-)

I tried this installation over two months ago and it was not working (this issue was also closed by that time, but the error was identical using conda-forge)

goanpeca · 2019-05-29T23:33:47Z

@orbeckst

$ conda create -n mda mdanalysis python=3.7 -c conda-forge
$ conda activate mda
$ python
>>>from MDAnalysis.tests.datafiles import PSF, DCD   # test trajectory

Results in

*** ERROR ***
In order to run the MDAnalysis test cases you must install the
MDAnalysisTestData package (which has been separated from the 
library code itself since release 0.7.4). Go to 

     http://pypi.python.org/pypi/MDAnalysisTests

and download and install the `MDAnalysisTests-x.y.z.tar.gz'
that matches your MDAnalysis release.
Traceback (most recent call last):
  File "/Users/gpena-castellanos/anaconda2/envs/mda/lib/python3.7/site-packages/MDAnalysis/tests/datafiles.py", line 41, in <module>
    from MDAnalysisTests.datafiles import *
ModuleNotFoundError: No module named 'MDAnalysisTests'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/gpena-castellanos/anaconda2/envs/mda/lib/python3.7/site-packages/MDAnalysis/tests/datafiles.py", line 52, in <module>
    raise ImportError("MDAnalysisTests package not installed.")
ImportError: MDAnalysisTests package not installed.

Which talks about pip and would confuse users using conda

(BTW before I could not import the package, not sure what changed)

kain88-de · 2019-05-30T10:27:15Z

The warning you get is normal. The test files are in a separate package mdanalysistests that has to be installed as well. I agree that the hint to pypi should be changed to the mdanalysis homepage where we link against current installation with pip or conda.

goanpeca · 2019-05-30T11:55:54Z

The warning you get is normal.

yep!

Agreed. Will need to test on the system I got the issue with python 3. Glad to see it is working for me now :-)

orbeckst added installation Python3 labels Jun 29, 2017

orbeckst added the defect label Jun 29, 2017

kain88-de mentioned this issue Jun 30, 2017

package is installable on python 3 conda-forge/mdanalysis-feedstock#4

Closed

kain88-de closed this as completed Jul 18, 2017

goanpeca mentioned this issue May 29, 2019

Use a explicit iteration scheme #2269

Closed

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Conda installation in a Python 3 environment doesn't work #1446

Conda installation in a Python 3 environment doesn't work #1446

khinsen commented Jun 29, 2017

kain88-de commented Jun 29, 2017

khinsen commented Jun 29, 2017

kain88-de commented Jun 29, 2017

kain88-de commented Jun 29, 2017

orbeckst commented Jun 29, 2017

orbeckst commented Jun 29, 2017 •

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khinsen commented Jun 30, 2017

kain88-de commented Jul 18, 2017

goanpeca commented Mar 11, 2019

orbeckst commented May 29, 2019 •

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goanpeca commented May 29, 2019

goanpeca commented May 29, 2019 •

edited

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kain88-de commented May 30, 2019

goanpeca commented May 30, 2019

Conda installation in a Python 3 environment doesn't work #1446

Conda installation in a Python 3 environment doesn't work #1446

Comments

khinsen commented Jun 29, 2017

Expected behaviour

Actual behaviour

kain88-de commented Jun 29, 2017

khinsen commented Jun 29, 2017

kain88-de commented Jun 29, 2017

kain88-de commented Jun 29, 2017

orbeckst commented Jun 29, 2017

orbeckst commented Jun 29, 2017 • edited Loading

khinsen commented Jun 30, 2017

kain88-de commented Jul 18, 2017

goanpeca commented Mar 11, 2019

orbeckst commented May 29, 2019 • edited Loading

goanpeca commented May 29, 2019

goanpeca commented May 29, 2019 • edited Loading

kain88-de commented May 30, 2019

goanpeca commented May 30, 2019

orbeckst commented Jun 29, 2017 •

edited

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orbeckst commented May 29, 2019 •

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goanpeca commented May 29, 2019 •

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