pyemma.util no attribute 'context'

[pojeda]

Hi,

I installed pyEMMA (2.5.11) with pip. I tried the test case described here http://emma-project.org/latest/tutorials/notebooks/00-pentapeptide-showcase.html#Feature-selection with my own Gromacs trajectory. Then, I get the error message:

AttributeError: module 'pyemma.util' has no attribute 'contexts'

Do you have any comments on this error?

/Pedro

pip list: Package Version

---

alabaster 0.7.12 appdirs 1.4.4 asn1crypto 1.4.0 asttokens 2.0.5 astunparse 1.6.3 atomicwrites 1.4.0 attrs 21.2.0 Babel 2.9.1 backcall 0.2.0 backports.entry-points-selectable 1.1.0 backports.functools-lru-cache 1.6.4 bcrypt 3.2.0 bhmm 0.6.3 bitstring 3.1.9 blist 1.3.6 CacheControl 0.12.6 cachy 0.3.0 certifi 2021.5.30 cffi 1.14.6 chardet 4.0.0 charset-normalizer 2.0.4 cleo 0.8.1 click 8.0.1 clikit 0.6.2 colorama 0.4.4 crashtest 0.3.1 cryptography 3.4.7 cycler 0.11.0 Cython 0.29.24 decorator 5.0.9 deeptime 0.4.2 dill 0.3.5.1 distlib 0.3.2 docopt 0.6.2 docutils 0.17.1 ecdsa 0.17.0 executing 0.8.3 filelock 3.0.12 flit 3.3.0 flit_core 3.3.0 fonttools 4.33.3 fsspec 2021.7.0 future 0.18.2 glob2 0.7 h5py 3.7.0 html5lib 1.1 humanfriendly 10.0 idna 3.2 imagesize 1.2.0 importlib-metadata 4.6.3 importlib-resources 5.2.2 iniconfig 1.1.1 intervaltree 3.1.0 intreehooks 1.0 ipaddress 1.0.23 ipython 8.4.0 jedi 0.18.1 jeepney 0.7.1 Jinja2 3.0.1 joblib 1.0.1 jsonschema 3.2.0 keyring 21.2.0 keyrings.alt 4.1.0 kiwisolver 1.4.2 liac-arff 2.5.0 lockfile 0.12.2 MarkupSafe 2.0.1 matplotlib 3.5.2 matplotlib-inline 0.1.3 mdshare 0.4.2 mdtraj 1.9.7 mock 4.0.3 more-itertools 8.8.0 msgpack 1.0.2 msmtools 1.2.6 multiprocess 0.70.13 netaddr 0.8.0 netifaces 0.11.0 nose 1.3.7 numpy 1.22.4 packaging 20.9 paramiko 2.7.2 parso 0.8.3 pastel 0.2.1 pathlib2 2.3.6 pathos 0.2.9 paycheck 1.0.2 pbr 5.6.0 pexpect 4.8.0 pickleshare 0.7.5 Pillow 9.1.1 pip 22.1.2 pkginfo 1.7.1 platformdirs 2.2.0 pluggy 0.13.1 poetry 1.1.7 poetry-core 1.0.3 pox 0.3.1 ppft 1.7.6.5 prompt-toolkit 3.0.29 psutil 5.8.0 ptyprocess 0.7.0 pure-eval 0.2.2 py 1.10.0 py-expression-eval 0.3.13 pyasn1 0.4.8 pycparser 2.20 pycrypto 2.6.1 pyEMMA 2.5.11 Pygments 2.9.0 pylev 1.4.0 PyNaCl 1.4.0 pyparsing 2.4.7 pyrsistent 0.18.0 pytest 6.2.4 python-dateutil 2.8.2 pytoml 0.1.21 pytz 2021.1 PyYAML 6.0 regex 2021.8.3 requests 2.26.0 requests-toolbelt 0.9.1 scandir 1.10.0 scikit-learn 1.1.1 scipy 1.8.1 SecretStorage 3.3.1 semantic-version 2.8.5 setuptools 62.1.0 setuptools-rust 0.12.1 setuptools-scm 6.0.1 shellingham 1.4.0 simplegeneric 0.8.1 simplejson 3.17.3 six 1.16.0 snowballstemmer 2.1.0 sortedcontainers 2.4.0 Sphinx 4.1.2 sphinx-bootstrap-theme 0.7.1 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.5 sphinxcontrib-websupport 1.2.4 stack-data 0.2.0 tabulate 0.8.9 threadpoolctl 2.2.0 toml 0.10.2 tomlkit 0.7.2 tqdm 4.64.0 traitlets 5.2.2.post1 typing-extensions 3.10.0.0 ujson 4.0.2 urllib3 1.26.6 virtualenv 20.7.0 wcwidth 0.2.5 webencodings 0.5.1 wheel 0.37.1 xlrd 2.0.1 zipfile36 0.1.3 zipp 3.5.0

[clonker]

Hi, sorry for the super late response. You can add a import pyemma.util.contexts to the beginning of the notebook, then it should work fine. We have to fix this in the example.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[yihengwuKP]

Thanks for posting the solution. I would still prefer if the documentation is changed accordingly so that in the future it's easier for people to run the tutorial.

[clonker]

Definitely. Unfortunately I do not have access to the hosting servers anymore. Generally this project has gone a bit stale and probably will soon be deprecated in favor of deeptime (deeptime-ml/deeptime).