adaptivemd

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Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 3.5.1 to 4.6.3. Release notes Sourced from pymongo's releases. PyMongo 4.6.2 Release notes: https://www.mongodb.com/community/forums/t/pymongo-4-6-2-released/267404 PyMongo 4.6.1 Release notes: https://www.mongodb.com/community/forums/t/pymongo-4-6-1-released/255752 PyMongo 4.6.0 Release notes: https://www.mongodb.com/community/forums/t/pymongo-4-6-0-released/251866 PyMongo 4.5.0 Release...

dependabot[bot]

Unit tests fail when running them on my local resource, apparently some paths are not well configured. I get the following errorwith test_simple_wrapped.py and test_simple_wrapped.py: IOError: [Errno 2] No such...

thempel

PyEMMA's support for python 2 will soon expire (also, python 2's end of life is coming closer). That means that we need python 3 support.

thempel

Tutorial 5 not working

9

Using one's own generator class, i.e. for implementing a pyemma analysis script, does not work as described in notebook 5. First, their are several bugs in the notebook itself. Substituting...

thempel

Simple test in README.md does not work

2

The simple test in the README doesn't work: # run a simple test cd adaptive/tests/ python test_simple.py 1) The directory name is wrong. It should be 'adaptivemd/tests/' 2) The MongoDB...

eblen

Just a list of features we think are useful... - support for FeatureTrajectories (I think I had this almost figured out and ready). A clean way to generate Trajectory Files...

jhprinz

mongodb available in Anaconda distribution

1

I've just noticed, that mongodb is now available for conda install. Should we update the install instructions accordingly for the sake of an easier installation process? Note that the available...

marscher

Existing traj integration

2

This is the documentation on how to add existing trajectories. It includes a few fixes that were necessary: - For multiple engines in a pyemma analysis, file names have to...

thempel

Refers to: https://github.com/markovmodel/adaptivemd/blob/master/examples/tutorial/4_example_advanced_tasks.ipynb But addresses also general package/API issues along the way. I'll have a number of questions / comments about the details of this notebook, but first of all...

franknoe

This refers to https://github.com/markovmodel/adaptivemd/blob/master/examples/tutorial/3_example_adaptive.ipynb While I'm working through the notebook, some of the questions / comments refer to the framework in general. Apologies if I am making comments or asking...

franknoe