Hi,

Some tutorial notebooks have this LaTeX rendering issue:

These are the notebooks that I see the problem:

• http://www.emma-project.org/v2.5.5/generated/05-pcca-tpt.html
• http://www.emma-project.org/v2.5.5/generated/07-hidden-markov-state-models.html

Apparently, the absolute path of the Travis build is used (/home/travis/...) instead of the relative path to the current page.

For example, Fs Peptide (in RAM) links (in the bottom) to [this page](http://msmbuilder.org/home/travis/build/msmbuilder/msmbuilder/docs/_build/html/examples/Fs-Peptide-in-RAM/Fs-Peptide-in-RAM.ipynb

As the subject says, having to hunt a supplementary table in a manuscript to see what an abbreviation indicates is awkward (and, IIRC, there is no "supplementary table 2" in the TitanCNA paper).

Ideally this should be in the README.md or in the repo (or in the help files).

======================================================================
FAIL: test_discrete_4_2 (bhmm.tests.test_init_discrete.TestHMM)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/_test/lib/python3.5/site-packages/bhmm-0.6.1+22.g6f0de1e-py3.5-linux-x86_64.egg/bhmm/tests/test_init_discrete.py", line

When I run this:

from leuvenmapmatching.map.inmem import InMemMap

map_con = InMemMap("myosm", use_latlon=True, use_rtree=True, index_edges=True)

I get this warning:

/home/user/anaconda3/envs/ox/lib/python3.8/site-packages/pyproj/crs/crs.py:55: FutureWarning: '+init=<authority>:<code>' syntax is deprecated. '<authority>:<code>' is the preferred initialization method. When m

• Stable documentation published on new tag.
• Tags are created by TagBot -> this doesn't trigger the workflow.