AttributeError: 'module' object has no attribute 'popall'

[Cactusolo]

Hi ,
I have been using TreeTime: Maximum Likelihood Phylodynamics tt 0.7.4, with standard run treetime --tree iqtree_alnclen.tre --aln subiqtree.fasta --dates date_iqtree.csv. It was all good, but giving error as half-way.

The error msg is "AttributeError: 'module' object has no attribute 'popall'" as detailes, below. Any suggestions are appreciated.

Symmetrized rates from j->i (W_ij):
A C G T -
A 0 0.4601 1.8243 0.6456 7.8015
C 0.4601 0 0.3286 3.7665 8.3047
G 1.8243 0.3286 0 0.6436 6.2111
T 0.6456 3.7665 0.6436 0 7.3774

• 7.8015 8.3047 6.2111 7.3774 0

Actual rates from j->i (Q_ij):
A C G T -
A 0 0.1361 0.5396 0.191 2.3074
C 0.0819 0 0.0585 0.6703 1.4779
G 0.3503 0.0631 0 0.1236 1.1927
T 0.2094 1.2216 0.2087 0 2.3927

• 0.0774 0.0824 0.0616 0.0732 0

Inferred sequence evolution model (saved as 2020-04-01_treetime/molecular_clock.txt):
Root-Tip-Regression:
--rate: 9.280e-04
--r^2: 0.32

/home/.local/lib/python2.7/site-packages/matplotlib/colors.py:680: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1.
not cbook.is_string_like(colors[0]):
/home/.local/lib/python2.7/site-packages/matplotlib/lines.py:44: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1.
if is_string_like(style) and is_hashable(style):
/home/.local/lib/python2.7/site-packages/matplotlib/font_manager.py:971: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1.
if is_string_like(family):
/home/.local/lib/python2.7/site-packages/matplotlib/font_manager.py:697: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1.
if is_string_like(family):
/home/.local/lib/python2.7/site-packages/matplotlib/text.py:218: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1.
elif is_string_like(fontproperties):
Traceback (most recent call last):
File "/usr/local/bin/treetime", line 12, in
return_code = params.func(params)
File "/usr/local/lib/python2.7/dist-packages/treetime/argument_parser.py", line 213, in toplevel
timetree(params)
File "/usr/local/lib/python2.7/dist-packages/treetime/wrappers.py", line 607, in timetree
confidence=0.9 if calc_confidence else None)
File "/usr/local/lib/python2.7/dist-packages/treetime/treetime.py", line 829, in plot_vs_years
ax = plt.subplot(111)
File "/home/.local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 1044, in subplot
a = fig.add_subplot(*args, **kwargs)
File "/home/.local/lib/python2.7/site-packages/matplotlib/figure.py", line 1021, in add_subplot
a = subplot_class_factory(projection_class)(self, *args, **kwargs)
File "/home/.local/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 73, in init
self._axes_class.init(self, fig, self.figbox, **kwargs)
File "/home/.local/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 529, in init
self._init_axis()
File "/home/.local/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 622, in _init_axis
self.xaxis = maxis.XAxis(self)
File "/home/.local/lib/python2.7/site-packages/matplotlib/axis.py", line 676, in init
self.cla()
File "/home/.local/lib/python2.7/site-packages/matplotlib/axis.py", line 760, in cla
self.reset_ticks()
File "/home/.local/lib/python2.7/site-packages/matplotlib/axis.py", line 771, in reset_ticks
cbook.popall(self.majorTicks)
AttributeError: 'module' object has no attribute 'popall'

Miao

[Cactusolo]

OK, it was resolved by sudo apt-get install python-matplotlib.
[In case others needed]