Version mismatch between pymc3 and theano-pymc3

Questions
1

I have tried installing pymc3 and theano-pymc3. I cloned the repository and then

pip install -r requirements.txt

got the followng error message:

at the end. I did save the full output if needed by someone

Using legacy ‘setup.py install’ for theano-pymc, since package ‘wheel’ is not installed.
Installing collected packages: theano-pymc
Attempting uninstall: theano-pymc
Found existing installation: Theano-PyMC 1.0.11
Uninstalling Theano-PyMC-1.0.11:
Successfully uninstalled Theano-PyMC-1.0.11
Running setup.py install for theano-pymc … done
ERROR: pip’s dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
pymc3 3.10.0 requires theano-pymc==1.0.11, but you have theano-pymc 1.1.2 which is incompatible.
Successfully installed theano-pymc-1.1.2

2

It does look like it worked correctly, did you try importing pymc3?

Also, we strongly recommend using conda to install as it’s really hard to install Theano in a way that correctly uses the system compilers and conda comes with its own.

3

if I try to import pymc3, I get

No module named ‘theano.gof’

I do have a conda account so I guess I will try that

thanks

4

You can get more details on installation here:

I think you have an old version of theano, so before anything I would pip uninstall theano.

5

the solution I eventually come up with was to use mini-forge
I run opensuse linux and am happy with their software management
Just plain conda was overkill for me
thanks for the help

6

Fresh conda environment and installed according to

Nevertheless, after installing BMLingam:

https://taku-y.github.io/bmlingam/installation.html

and running:

# bmlingam-causality sampledata.csv --result_dir=result

I got the aforementioned error message:

No module named ‘theano.gof’

7

Are you sure that installing blingam didn’t pull in an old PyMC3 version? Can you post the theano-pymc and pymc3 versions?

8

pymc3>=3.0.rc2

After a variety of attempts to get this installed in a variety of combinations of conda, pip, git and a variety of interventions in which versions were installed in what order…

I gave up and rewrote bmlingam to use v4.0.0. It was easy to install and get v4 running. Worked first time.

9

That’s great! Maybe do a PR to bmlingam so that others can use it.

10

I would except I made some modifications in the guts of bmlingam necessary to reduce the O(N^2) of its causal exploratory data analysis, that would not translate to others’ datasets. What I did was take advantage of a naming convention I use in my dataset to avoid pairs of variables that aren’t very informative. For example, each variable has a suffix on its name consisting of 4 digits specifying the year for which the variable was measured – to avoid intra-variable time-series causal calculations.

Perhaps there is a way of making this kind of thing general by providing a call-back, defaulting to None, to do pruning pairs.