When trying to install molpx using

conda install -n myenv molpx -c conda-forge

I am met with the message

Solving environment: failed

InvalidVersionSpecError: Invalid version spec: =2.7 

I also tried opening up a completely new environment in case I had some mismatching dependencies, but that resulted in the same message. I am on Linux, and have conda 4.5.11 and Python 3.6.13 installed. Happy to provide more information if that's needed!

conda info:

     active environment : linneaenv
    active env location : /home/user/.conda/envs/linneaenv
            shell level : 1
       user config file : /home/user/.condarc
 populated config files : /home/user/.condarc
          conda version : 4.5.11
    conda-build version : 3.15.1
         python version : 3.7.0.final.0
       base environment : /opt/scp/software/Anaconda3/5.3.0  (read only)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /opt/scp/software/Anaconda3/5.3.0/pkgs
                          /home/user/.conda/pkgs
       envs directories : /home/user/.conda/envs
                          /opt/scp/software/Anaconda3/5.3.0/envs
               platform : linux-64
             netrc file : None
           offline mode : False

I have had the same problem with other packages, but in that case it was enough to remove the conda-forge channel and add it again, with molpx this didn't work for me.

It's time we tackle this problem:

python setup.py develop 
running develop
running egg_info
writing molPX.egg-info/PKG-INFO
writing dependency_links to molPX.egg-info/dependency_links.txt
writing top-level names to molPX.egg-info/top_level.txt
writing requirements to molPX.egg-info/requires.txt
writing pbr to molPX.egg-info/pbr.json
reading manifest file 'molPX.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'molPX.egg-info/SOURCES.txt'
running build_ext
Creating /home/mi/gph82/miniconda3/lib/python3.4/site-packages/molPX.egg-link (link to .)
molPX 0.1.1+27.g18c03d1.dirty is already the active version in easy-install.pth

Installed /home/mi/gph82/SOURCE_gph82/python/molPX
Processing dependencies for molPX==0.1.1+27.g18c03d1.dirty
Searching for nglview>=0.6.2.2
Reading https://pypi.python.org/simple/nglview/
Best match: nglview 0.6.2.3
Downloading https://pypi.python.org/packages/8c/5d/caeb1505cc0a5b5307f1283f47b36fbdbe9df5b5b2f0a56df716dc50873c/nglview-0.6.2.3.tar.gz#md5=cbd42f3f5f6483e0dfef0ab40a483c06
Processing nglview-0.6.2.3.tar.gz
Writing /tmp/easy_install-nx7jf1y0/nglview-0.6.2.3/setup.cfg
Running nglview-0.6.2.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-nx7jf1y0/nglview-0.6.2.3/egg-dist-tmp-dhc6ltk7
setup.py entered
$PATH=/home/mi/gph82/miniconda3/bin:/home/mi/gph82/Downloads/myplumed/bin:/home/mi/gph82/Downloads/dowser/bin/linux:/home/mi/gph82/Downloads/dowser/bin:/home/mi/gph82/SOURCE_gph82/scripts:/home/mi/gph82/bin/vmd_gph82_bins:/home/mi/gph82/Gabedit:/usr/bin:/home/mi/gph82/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
package init file 'nglview/tests/__init__.py' not found (or not a regular file)
package init file 'nglview/staticlab/__init__.py' not found (or not a regular file)
warning: no files found matching 'nglview/js/*'
warning: no previously-included files matching '*.pycinclude' found anywhere in distribution
warning: no previously-included files matching '*.ipynb' found anywhere in distribution
warning: no previously-included files matching '*.gif' found anywhere in distribution
warning: no previously-included files matching '*tests/notebooks/*' found anywhere in distribution
UPDATING build/lib/nglview/_version.py
set build/lib/nglview/_version.py to '0.6.2.3'
Trying to enable extensions
error: SandboxViolation: rmdir('/home/mi/gph82/.local/share/jupyter/nbextensions/nglview-js-widgets',) {}

The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.

This package cannot be safely installed by EasyInstall, and may not
support alternate installation locations even if you run its setup
script by hand.  Please inform the package's author and the EasyInstall
maintainers to find out if a fix or workaround is available.

change the docs...

Many tests are failing because one method is supposed to find the two centers of a sampled bimodal distribution. The criterion of what constitutes having found the center should be relaxed or a more deterministc test should be devised

Hi,

I am using molPX 0.17 installed with anaconda on a Ubuntu computer. I have attached the results of conda_list conda_list.txt.

I am trying to run the clustering section of the example notebook 2.molPX_TICA_BPTI

When I run the 'Plot clusters' and 'Link the clusters positions with the molecular structures' sections (last cell of the clustering. I do not see any structure, just the FES plot with the cluster centers and the crosshair. I am guessing form the command in the cell that I am supposed to see the structures.

I have attached a screenshot of the notebook: .
Note the warning message:

/home/el14718/Software/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:6:RuntimeWarning: divide by zero encountered in log

And the [Out] section: (NGLWidget(count=5), <matplotlib.widgets.AxesWidget at 0x7fdfe3beaf60>)

Note also that the only modification to the notebook is that I change the order of the import in the first cell following issue #43:

%matplotlib ipympl
from matplotlib import pylab as plt
import molpx
import pyemma
import numpy as np

Many thanks

I am trying to link use the clustering as input as u declare in the tutorial "molPX and TICA with BPTI", but it seems that x not defined here.

Plot clusters

plt.figure(figsize=(4,4))
plt.plot(clkmeans.clustercenters[:,0], clkmeans.clustercenters[:,1],' ok')

FES as background is optional (change the bool to False)

if True:
plt.contourf(x[:-1], y[:-1], -np.log(h.T), alpha=.50)

Link the clusters positions with the molecular structures

linked_ngl_wdg = molpx.visualize.sample(data_sample,
geoms.superpose(geoms[0]),
plt.gca(),
clear_lines=False,
#plot_path=True
)
linked_ngl_wdg

Hello,

I was wondering if it is somehow possible to request an orthographic view of the structures displayed with molpx.visualize.FES for example.

I know this is possible with NGLView using something like :

view.camera = 'orthographic'

http://nglviewer.org/nglview/latest/index.html?highlight=orthographic

But I don't know if it is possible to somehow specify that option in molPX.
If it is not implemented, I believe that would be a nice addition as the perspective view is very often misleading, especially when looking at neighbouring conformations on the FES.

Many thanks in advance!

It seems we're suffering from this nglviewer/nglview#584

in these tests:
https://travis-ci.org/markovmodel/molPX/builds/211010110
where this combination does not work
nglview: 0.6.2.2-py27_1
ipywidgets: 6.0.0-py27_0

because ipywidgets>=6 requires nglview>=0.6.2.3

I'm assuming because nglview>=0.6.2.3 is not yet in omnia? @marscher any help will be welcome

I am trying to run the example file which is given in http://molpx.readthedocs.io/en/stable/Projection_Explorer_Copy.html I am getting following error

TraitError Traceback (most recent call last)
~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
2251 try:
-> 2252 v = self._trait._validate(obj, v)
2253 except TraitError:

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
590 if hasattr(self, 'validate'):
--> 591 value = self.validate(obj, value)
592 if obj._cross_validation_lock is False:

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in validate(self, obj, value)
1676 else:
-> 1677 self.error(obj, value)
1678

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in error(self, obj, value)
1523
-> 1524 raise TraitError(e)
1525

TraitError: The 'None' trait of a MolPXHBox instance must be a Widget, but a value of class 'matplotlib.backends.backend_agg.FigureCanvasAgg' (i.e. <matplotlib.backends.backend_agg.FigureCanvasAgg object at 0x7fddb7133898>) was specified.

During handling of the above exception, another exception occurred:

TraitError Traceback (most recent call last)
in ()
6 #Y,
7 nbins=50,
----> 8 proj_idxs=[1,2],
9 # axlabel='TIC',
10 )

~/miniconda3/lib/python3.6/site-packages/molpx/visualize.py in FES(MD_trajectories, MD_top, projected_trajectories, proj_idxs, nbins, n_sample, proj_stride, weights, proj_labels, n_overlays, atom_selection, **sample_kwargs)
217 ax.figure.tight_layout()
218 axes_wdg.canvas.set_window_title("FES")
--> 219 outbox = _linkutils.MolPXHBox([ngl_wdg, axes_wdg.canvas])
220 _linkutils.auto_append_these_mpx_attrs(outbox, geoms, ax, _plt.gcf(), ngl_wdg, axes_wdg, data_sample)
221

~/miniconda3/lib/python3.6/site-packages/molpx/_linkutils.py in init(self, *args, **kwargs)
204 class MolPXHBox(_HBox, MolPXBox):
205 def init(self, *args, **kwargs):
--> 206 super(MolPXHBox, self).init(*args, **kwargs)
207 self.append_if_existing(args[0])
208

~/miniconda3/lib/python3.6/site-packages/ipywidgets/widgets/widget_box.py in init(self, children, **kwargs)
62 def init(self, children=(), **kwargs):
63 kwargs['children'] = children
---> 64 super(Box, self).init(**kwargs)
65 self.on_displayed(Box._fire_children_displayed)
66

~/miniconda3/lib/python3.6/site-packages/ipywidgets/widgets/widget.py in init(self, **kwargs)
409 """Public constructor"""
410 self._model_id = kwargs.pop('model_id', None)
--> 411 super(Widget, self).init(**kwargs)
412
413 Widget._call_widget_constructed(self)

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in init(self, *args, **kwargs)
995 for key, value in kwargs.items():
996 if self.has_trait(key):
--> 997 setattr(self, key, value)
998 else:
999 # passthrough args that don't set traits to super

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in set(self, obj, value)
583 raise TraitError('The "%s" trait is read-only.' % self.name)
584 else:
--> 585 self.set(obj, value)
586
587 def _validate(self, obj, value):

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in set(self, obj, value)
557
558 def set(self, obj, value):
--> 559 new_value = self._validate(obj, value)
560 try:
561 old_value = obj._trait_values[self.name]

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
589 return value
590 if hasattr(self, 'validate'):
--> 591 value = self.validate(obj, value)
592 if obj._cross_validation_lock is False:
593 value = self._cross_validate(obj, value)

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in validate(self, obj, value)
2240 return value
2241
-> 2242 value = self.validate_elements(obj, value)
2243
2244 return value

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
2252 v = self._trait._validate(obj, v)
2253 except TraitError:
-> 2254 self.element_error(obj, v, self._trait)
2255 else:
2256 validated.append(v)

~/miniconda3/lib/python3.6/site-packages/traitlets/traitlets.py in element_error(self, obj, element, validator)
2231 e = "Element of the '%s' trait of %s instance must be %s, but a value of %s was specified."
2232 % (self.name, class_of(obj), validator.info(), repr_type(element))
-> 2233 raise TraitError(e)
2234
2235 def validate(self, obj, value):

TraitError: Element of the 'children' trait of a MolPXHBox instance must be a Widget, but a value of <matplotlib.backends.backend_agg.FigureCanvasAgg object at 0x7fddb7133898> <class 'matplotlib.backends.backend_agg.FigureCanvasAgg'> was specified.

Can you please help me in resolving this error

with regards
Singam

Thanks for submitting an issue!

Here's a quick checklist of what to include:

• Include a detailed description of the bug or suggestion, optionally with a copy of the output/Exception
• pip list or conda list of the environment you are using (please attach a txt file to the issue).
• molPX version and operating system versions
• Minimal example if possible, a Python script, zipped input data (if not too large)

Currently the notebooks are contained in the package, but there is no API to access them. If the only purpose of this organization is to provide them for the generation of documentation, I suggest to store them outside for the sake of a smaller package.

We can also consider a small command/ api function to start the notebook and play around with it.

Currently the user can only guess from the notebooks that he/she needs to use ipympl as matplotlib backend to get things working. We should consider using a context manager to temporarily set ipympl as backend and return to the users default. This would have the advantage of minimal interference and will not use a lot of memory for plots which are intended not to be interactive.

the di-ala example notebook raises this upon creation of the widget:

@gph82 have you seen this error before? Does it block the release right now? We shouldn't rel a non-working version IMHO.

--------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-7-cd6ac4d4024a> in <module>()
      5                                   proj_labels=['$\phi$',
      6                                                '$\psi$'],
----> 7                                   atom_selection="symbol != H",
      8                                   #proj_idxs=[1],
      9                                   #n_overlays=5,

~/miniconda3/envs/molpx/lib/python3.6/site-packages/molpx/visualize.py in FES(MD_trajectories, MD_top, projected_trajectories, proj_idxs, nbins, n_sample, proj_stride, weights, proj_labels, n_overlays, atom_selection, **sample_kwargs)
    217     ax.figure.tight_layout()
    218     axes_wdg.canvas.set_window_title("FES")
--> 219     outbox = _linkutils.MolPXHBox([ngl_wdg, axes_wdg.canvas])
    220     _linkutils.auto_append_these_mpx_attrs(outbox, geoms, ax, _plt.gcf(), ngl_wdg, axes_wdg, data_sample)
    221 

~/miniconda3/envs/molpx/lib/python3.6/site-packages/molpx/_linkutils.py in __init__(self, *args, **kwargs)
    204 class MolPXHBox(_HBox, MolPXBox):
    205     def __init__(self, *args, **kwargs):
--> 206         super(MolPXHBox, self).__init__(*args, **kwargs)
    207         self.append_if_existing(args[0])
    208 

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipywidgets/widgets/widget_box.py in __init__(self, children, **kwargs)
     61     def __init__(self, children=(), **kwargs):
     62         kwargs['children'] = children
---> 63         super(Box, self).__init__(**kwargs)
     64         self.on_displayed(Box._fire_children_displayed)
     65 

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipywidgets/widgets/widget.py in __init__(self, **kwargs)
    410 
    411         Widget._call_widget_constructed(self)
--> 412         self.open()
    413 
    414     def __del__(self):

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipywidgets/widgets/widget.py in open(self)
    433                 args['comm_id'] = self._model_id
    434 
--> 435             self.comm = Comm(**args)
    436 
    437     @observe('comm')

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/comm/comm.py in __init__(self, target_name, data, metadata, buffers, **kwargs)
     55             if self.primary:
     56                 # I am primary, open my peer.
---> 57                 self.open(data=data, metadata=metadata, buffers=buffers)
     58             else:
     59                 self._closed = False

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/comm/comm.py in open(self, data, metadata, buffers)
     92                               data=data, metadata=metadata, buffers=buffers,
     93                               target_name=self.target_name,
---> 94                               target_module=self.target_module,
     95                               )
     96             self._closed = False

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/comm/comm.py in _publish_msg(self, msg_type, data, metadata, buffers, **keys)
     63         data = {} if data is None else data
     64         metadata = {} if metadata is None else metadata
---> 65         content = json_clean(dict(data=data, comm_id=self.comm_id, **keys))
     66         self.kernel.session.send(self.kernel.iopub_socket, msg_type,
     67             content,

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/jsonutil.py in json_clean(obj)
    189         out = {}
    190         for k,v in iteritems(obj):
--> 191             out[unicode_type(k)] = json_clean(v)
    192         return out
    193     if isinstance(obj, datetime):

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/jsonutil.py in json_clean(obj)
    189         out = {}
    190         for k,v in iteritems(obj):
--> 191             out[unicode_type(k)] = json_clean(v)
    192         return out
    193     if isinstance(obj, datetime):

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/jsonutil.py in json_clean(obj)
    189         out = {}
    190         for k,v in iteritems(obj):
--> 191             out[unicode_type(k)] = json_clean(v)
    192         return out
    193     if isinstance(obj, datetime):

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/jsonutil.py in json_clean(obj)
    175 
    176     if isinstance(obj, list):
--> 177         return [json_clean(x) for x in obj]
    178 
    179     if isinstance(obj, dict):

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/jsonutil.py in <listcomp>(.0)
    175 
    176     if isinstance(obj, list):
--> 177         return [json_clean(x) for x in obj]
    178 
    179     if isinstance(obj, dict):

~/miniconda3/envs/molpx/lib/python3.6/site-packages/ipykernel/jsonutil.py in json_clean(obj)
    195 
    196     # we don't understand it, it's probably an unserializable object
--> 197     raise ValueError("Can't clean for JSON: %r" % obj)

ValueError: Can't clean for JSON: <matplotlib.backends.backend_agg.FigureCanvasAgg object at 0x7f47e8c50320>

I just created a new environment to test ipywidgets 6:

conda create --name python3.6_for_ipywidgets6 python=3.6

Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6:

The following NEW packages will be INSTALLED:

    openssl:    1.0.2k-1     
    pip:        9.0.1-py36_1 
    python:     3.6.0-0      
    readline:   6.2-2        
    setuptools: 27.2.0-py36_0
    sqlite:     3.13.0-0     
    tk:         8.5.18-0     
    wheel:      0.29.0-py36_0
    xz:         5.2.2-1      
    zlib:       1.2.8-3      

Proceed ([y]/n)? y

#
# To activate this environment, use:
# > source activate python3.6_for_ipywidgets6
#
# To deactivate this environment, use:
# > source deactivate python3.6_for_ipywidgets6
#

gph82@southsea:  ~$ source activate python3.6_for_ipywidgets6

and tried to install molpx first. Two things happen (please scroll till the bottom)

1. pip install molpx fails on installing mdtraj, even mdtraj fails on installing alone

pip install mdtraj 
Collecting mdtraj
  Downloading mdtraj-1.8.0.zip (20.2MB)
    100% |################################| 20.2MB 47kB/s 
    Complete output from command python setup.py egg_info:
    --------------------------------------------------------------------------------
    Error: building mdtraj requires numpy and cython>=0.19
    
    Try running the command ``pip install numpy cython`` or
    ``conda install numpy cython``.
    
    or see http://docs.scipy.org/doc/numpy/user/install.html and
    http://cython.org/ for more information.
    
    If you're feeling lost, we recommend downloading the (free) Anaconda python
    distribution https://www.continuum.io/downloads, because it comes with
    these components included.
    --------------------------------------------------------------------------------
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-tmlqsnoy/mdtraj/

2. after installing it myself via conda install mdtraj -c omnia, then in pip install molpx no problem until but:

Python 3.6.0 |Continuum Analytics, Inc.| (default, Dec 23 2016, 12:22:00) 
Type "copyright", "credits" or "license" for more information.

IPython 5.3.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import molpx
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-84cce9d22026> in <module>()
----> 1 import molpx

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/molpx/__init__.py in <module>()
     10 
     11 from . import generate
---> 12 from . import visualize
     13 from .nbtools import example_notebook, _molpxdir
     14 

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/molpx/visualize.py in <module>()
     12 
     13 from matplotlib import pylab as _plt
---> 14 import nglview as _nglview
     15 import mdtraj as _md
     16 from os.path import basename as _basename

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/nglview/__init__.py in <module>()
     35 # interface
     36 from .config import BACKENDS
---> 37 from .widget import NGLWidget
     38 from .base_adaptor import *
     39 from .adaptor import *

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/nglview/widget.py in <module>()
      7 import numpy as np
      8 from IPython.display import display
----> 9 from ipywidgets import DOMWidget, widget_image
     10 from traitlets import (Unicode, Bool, Dict, List, Int, Integer, observe,
     11                        CaselessStrEnum)

ModuleNotFoundError: No module named 'ipywidgets'

I'm assuming 1) is this related to this: mdtraj/mdtraj#1119, shouldn't 2) be required by nglview itself?

Hi! Since mdtraj dropped their py2 support on win and so has nglview, (nglviewer/nglview#587 (comment)) I think we should drop it here as well.

I just noticed, that the callbacks for updating the widgets are executed for every movement of the mouse in the free energy landscape plot, no matter if the position is actually committed by click. This leads to degraded performance (maybe I should buy new hardware too).
It should be possible to update only if something is really changed and we need to recompute/redraw.

Example here:
https://travis-ci.org/markovmodel/molPX/jobs/217624733#L328

Could not find a tag or branch 'coverage', assuming commit.
error: pathspec 'coverage' did not match any file(s) known to git.

Command "git checkout -q coverage" failed with error code 1 in /private/var/folders/my/m6ynh3bn6tq06h7xr3js0z7r0000gn/T/pip-WeOdoD-build

Hi @marscher!

EDIT: I just pulled from master

IDK when this was introduced, but

sphinx-build -b html -d build/doctrees   source build/html
Running Sphinx v1.5.1

Exception occurred:
  File "/home/mi/gph82/SOURCE_gph82/python/molPX/molpx/bmutils.py", line 20, in <module>
    from pyemma.coordinates.transform import TICA as _TICA, PCA as _PCA
ImportError: No module named 'pyemma.coordinates.transform'
The full traceback has been saved in /tmp/sphinx-err-zygcu_h7.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Makefile:53: recipe for target 'html' failed
make: *** [html] Error 1

Is it possible that for the local build we have to add pyemma etc to the path in conf.py?

apologies if I've missed it in the doc's - but is there a way you want molPX cited?

• publish on Conda channels

  • omnia
  • conda-forge

• PyPI release

bioconda (uses a noarch_python package for nglview, which cause some trouble eg. on Windows). We currently do not support bioconda, since it would involve maintaining pyemma+all of its dependencies there.

Noarch issue:
conda/conda-build#1028

Omnia variant of nglview has a different version scheme (included tag prefix). This cause trouble if one wants to specify the same version no matter which channel is selected.

I am trying to execute the following part in BPTI TICA example

mpx_wdg_box = molpx.visualize.FES(MD_list,
                                 #MD_trajfiles,
                                 top,
                                 Y_filenames,
                                 #Y,
                                 nbins=50,
                                 #proj_idxs=[1,2],
                                 proj_labels='TIC',
                                 #n_overlays=5,
                                )
mpx_wdg_box

However I am getting the following error

AttributeError                            Traceback (most recent call last)
Cell In [4], line 1
----> 1 mpx_wdg_box = molpx.visualize.FES(MD_list,
      2                                  #MD_trajfiles,
      3                                  top,
      4                                  Y_filenames,
      5                                  #Y,
      6                                  nbins=50,
      7                                  #proj_idxs=[1,2],
      8                                  proj_labels='TIC',
      9                                  #n_overlays=5,
     10                                 )
     11 mpx_wdg_box

File ~/opt/anaconda3/envs/msmbuilder2022/lib/python3.9/site-packages/molpx/visualize.py:218, in FES(MD_trajectories, MD_top, projected_trajectories, proj_idxs, nbins, n_sample, proj_stride, weights, proj_labels, n_overlays, atom_selection, **sample_kwargs)
    216 ngl_wdg._set_size(*['%fin' % inches for inches in ax.get_figure().get_size_inches()])
    217 ax.figure.tight_layout()
--> 218 axes_wdg.canvas.set_window_title("FES")
    219 outbox = _linkutils.MolPXHBox([ngl_wdg, axes_wdg.canvas])
    220 _linkutils.auto_append_these_mpx_attrs(outbox, geoms, ax, _plt.gcf(), ngl_wdg, axes_wdg, data_sample)

AttributeError: 'Canvas' object has no attribute 'set_window_title'

Is it some version problem? Any help will be highly appreciated?

@marscher any idea? It was a problem with the coverage reporting, I remember we devoted some time to this but got nowhere...

I have two trajectories:
trajj=['strip_prod.dcd','strip_prod2.dcd']; each trajectory file includes 4797 frames.
data = pyemma.coordinates.load(trajj, features=feat)
Then I did TICA and k-means clustering, and I would like to visualize the structure of each cluster using molPX.
tica = pyemma.coordinates.tica(data,lag=8)
tica_concatenated = np.concatenate(tica.get_output())
data_sample, geoms = molpx.generate.sample(trajj, pdb, cluster,
n_geom_samples=100,
#keep_all_samples=True # read the doc for this argument
)
I got the error:
ValueError: largest specified index (9493.0 * stride=9493.0 * 1=9493) is larger than trajectory length 'strip_prod.dcd' = 4797

I was wondering where the specified index comes from and how to solve it. Thank you in advance!!