Conflicting Python resources and virtualenvs about american-gut

[wasade]

I thought setup.py specified IPython<4.0.0?
On Nov 10, 2015 11:36 PM, "J W Debelius" [email protected] wrote:

I tried to run Daniel's notebooks tonight (11/10). The ipymd release I got
(ipymd==0.1.1) required IPython 4.0 or greater. The code in mod2_pcoa.py
would not run with IPython > 4.0:

Traceback (most recent call last):
File "/Users/jwdebelius/.virtualenvs/test_env/bin/mod2_pcoa.py", line 4, in
import('pkg_resources').require('americangut==0.0.1')
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 3018, in
working_set = WorkingSet._build_master()
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 614, in _build_master
return cls._build_from_requirements(requires)
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 627, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 805, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: IPython<4.0.0

I did downgrade my matplotlib to 1.4, and this is a function which calls
seaborn, but the error isn't related to those packages.

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#180.

[jwdebelius]

To run ipymd as installed by setup.py I had to get the latest version of Jupyter.

On Nov 11, 2015, at 6:49 AM, Daniel McDonald [email protected] wrote:

I thought setup.py specified IPython<4.0.0?
On Nov 10, 2015 11:36 PM, "J W Debelius" [email protected] wrote:

I tried to run Daniel's notebooks tonight (11/10). The ipymd release I got
(ipymd==0.1.1) required IPython 4.0 or greater. The code in mod2_pcoa.py
would not run with IPython > 4.0:

Traceback (most recent call last):
File "/Users/jwdebelius/.virtualenvs/test_env/bin/mod2_pcoa.py", line 4, in
import('pkg_resources').require('americangut==0.0.1')
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 3018, in
working_set = WorkingSet._build_master()
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 614, in _build_master
return cls._build_from_requirements(requires)
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 627, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py", line 805, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: IPython<4.0.0

I did downgrade my matplotlib to 1.4, and this is a function which calls
seaborn, but the error isn't related to those packages.

—
Reply to this email directly or view it on GitHub
#180.

—
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[wasade]

Can you try emulating how packages are installed in travis? Possible
setup.py is out of sync
To run ipymd as installed by setup.py I had to get the latest version of
Jupyter.

On Nov 11, 2015, at 6:49 AM, Daniel McDonald [email protected]
wrote:

I thought setup.py specified IPython<4.0.0?
On Nov 10, 2015 11:36 PM, "J W Debelius" [email protected] wrote:

I tried to run Daniel's notebooks tonight (11/10). The ipymd release I
got
(ipymd==0.1.1) required IPython 4.0 or greater. The code in mod2_pcoa.py
would not run with IPython > 4.0:

Traceback (most recent call last):
File "/Users/jwdebelius/.virtualenvs/test_env/bin/mod2_pcoa.py", line
4, in
import('pkg_resources').require('americangut==0.0.1')
File
"/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py",
line 3018, in
working_set = WorkingSet._build_master()
File
"/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py",
line 614, in _build_master
return cls._build_from_requirements(requires)
File
"/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py",
line 627, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File
"/Users/jwdebelius/.virtualenvs/test_env/lib/python2.7/site-packages/pkg_resources/init.py",
line 805, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: IPython<4.0.0

I did downgrade my matplotlib to 1.4, and this is a function which calls
seaborn, but the error isn't related to those packages.

—
Reply to this email directly or view it on GitHub
#180.

—
Reply to this email directly or view it on GitHub.

—
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#180 (comment).

[jwdebelius]

I installed it according to travis, although I use virtualenv instead of conda as my enviroment manager. I installed the additional packages (numpy, lxml, and h5py), and then re-installed in the same directory.

I continue to get the error.

[wasade]

Sounds like your environment is not sane as the conda_requirements.txt clearly lists ipython<4.0.0. Suggest deleting your environment and recreating.

[jwdebelius]

I've built and rebuilt the environment several times using the directions provided in virtualenv. No change.

I think its critical we continue to support both conda and virtualenv with this package set up.

[wasade]

If the directions or install requirements are wrong, then they need to be
fixed. However, it is not clear what is wrong about them given this thread
which makes investigation impossible. This does deploy on many systems
including multiple distributions of Linux and OS X.

There is nothing here that indicates virtualenv is unsupported, or that an
environment manager is even required. There is nothing about this repo that
is conda specific. I strongly recommend switching to conda regardless
though as it vastly simplifies environment management.

Can you verify that there is nothing modifying $PYTHONPATH in your
environment prior to creating or activating an environment in any of your
login scripts (e.g., ~/.bash_profile)? And, can you verify that
executables such as ipython are not in your $PATH prior to creating or
activating an environment?

On Wed, Nov 11, 2015 at 3:59 PM, J W Debelius [email protected]
wrote:

I've built and rebuilt the environment several times using the directions
provided in virtualenv. No change.

I think its critical we continue to support both conda and virtualenv with
this package set up.

—
Reply to this email directly or view it on GitHub
#180 (comment)
.

[wasade]

I cannot recreate this issue. I used an empty environment, installed numpy
and h5py separately as is necessary for qiime via pypi, and did "pip
install -e ." I suspect that there is confusion in your environment
external to a manager.

On Wed, Nov 11, 2015 at 4:26 PM, Daniel T. McDonald <
[email protected]> wrote:

If the directions or install requirements are wrong, then they need to be
fixed. However, it is not clear what is wrong about them given this thread
which makes investigation impossible. This does deploy on many systems
including multiple distributions of Linux and OS X.

There is nothing here that indicates virtualenv is unsupported, or that an
environment manager is even required. There is nothing about this repo that
is conda specific. I strongly recommend switching to conda regardless
though as it vastly simplifies environment management.

Can you verify that there is nothing modifying $PYTHONPATH in your
environment prior to creating or activating an environment in any of your
login scripts (e.g., ~/.bash_profile)? And, can you verify that
executables such as ipython are not in your $PATH prior to creating or
activating an environment?

On Wed, Nov 11, 2015 at 3:59 PM, J W Debelius [email protected]
wrote:

I've built and rebuilt the environment several times using the directions
provided in virtualenv. No change.

I think its critical we continue to support both conda and virtualenv
with this package set up.

—
Reply to this email directly or view it on GitHub
#180 (comment)
.