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choderalab / assaytools

Modeling and Bayesian analysis of fluorescence and absorbance assays.
http://assaytools.readthedocs.org
GNU Lesser General Public License v2.1
18 stars 11 forks source link

Missing dependencies #109

Open MehtapIsik opened 7 years ago

MehtapIsik commented 7 years ago

While installing assaytools in a Python 3.5 environment I noticed some dependencies are missing. I had to install lxml, seaborn and pymc separately after running python setup.py install.

I noticed that those missing dependencies are actually listed in setup.py, but commented out: https://github.com/choderalab/assaytools/blob/master/setup.py#L87

I want to activate those lines so that these dependencies are also installed at setup.

MehtapIsik commented 7 years ago

@sonyahanson @jchodera Do you have any reservations about this change?

jchodera commented 7 years ago

These packages are not all pip-installable. If you uncomment them, you will no longer be able to install assaytools via python setup.py install because it will try (and fail) to install them by pip if you do not have them already installed.

We do have these listed in the conda package requirements, which is why we recommend people install this tool via conda. We haven't cut a release in quite some time, however.

MehtapIsik commented 7 years ago

@jchodera Thanks for explaining why those are commented out.

Do your recommend installing through conda and uninstalling to just get dependencies, and then installing assaytools from repository via python setup.py install ?

When I tried conda installing assaytools with conda, it gives an error about Python 3.5 incompatibility.

$ conda install assaytools
Fetching package metadata .............
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - assaytools -> python 2.7*
  - python 3.5*
Use "conda info <package>" to see the dependencies for each package.

I think we must update the conda release, so that it at least works with Python 3.5.

jchodera commented 7 years ago

Do your recommend installing through conda and uninstalling to just get dependencies, and then installing assaytools from repository via python setup.py install ?

Yes!

When I tried conda installing assaytools with conda, it gives an error about Python 3.5 incompatibility.

It looks like we haven't cut a new release since Python 3.5 was added. Let's create a new assaytools release.