You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I'm re-running some analysis with FAN-C and created a fresh virtual environment to install into. Using pip install fanc I installed the package and its dependencies. Automatically, matplotlib was installed to its latest version (3.9). However, the function register_cmap doesn't exist in matplotlib 3.9, so I had to manually downgrade to matplotlib 3.5.1.
Now I'm running into a problem with my pandas version (currently 2.2.2). Specifically:
Traceback (most recent call last):
File "/project/venv/bin/fanc", line 127, in <module>
Fanc()
File "/project/venv/bin/fanc", line 93, in __init__
command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
File "/project/venv/lib/python3.11/site-packages/fanc/commands/fanc_commands.py", line 1134, in pairs
restriction_site_distance_plot(pairs, ax=ax)
File "/project/venv/lib/python3.11/site-packages/fanc/plotting/statistics.py", line 179, in restriction_site_distance_plot
sns.distplot(distances, ax=ax, color=color, **kwargs)
File "/project/venv/lib/python3.11/site-packages/seaborn/distributions.py", line 2496, in distplot
kdeplot(**{axis: a}, ax=ax, color=kde_color, **kde_kws)
File "/project/venv/lib/python3.11/site-packages/seaborn/distributions.py", line 1701, in kdeplot
p.plot_univariate_density(
File "/project/venv/lib/python3.11/site-packages/seaborn/distributions.py", line 991, in plot_univariate_density
artist, = ax.plot(support, density, **artist_kws)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/project/venv/lib/python3.11/site-packages/matplotlib/axes/_axes.py", line 1632, in plot
lines = [*self._get_lines(*args, data=data, **kwargs)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/project/venv/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 312, in __call__
yield from self._plot_args(this, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/project/venv/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 487, in _plot_args
x = _check_1d(xy[0])
^^^^^^^^^^^^^^^^
File "/project/venv/lib/python3.11/site-packages/matplotlib/cbook/__init__.py", line 1327, in _check_1d
ndim = x[:, None].ndim
~^^^^^^^^^
File "/project/venv/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 5419, in __getitem__
disallow_ndim_indexing(result)
File "/project/venv/lib/python3.11/site-packages/pandas/core/indexers/utils.py", line 341, in disallow_ndim_indexing
raise ValueError(
ValueError: Multi-dimensional indexing (e.g. `obj[:, None]`) is no longer supported. Convert to a numpy array before indexing instead.
/project/venv/lib/python3.11/site-packages/tables/file.py:113: UnclosedFileWarning: Closing remaining open file: ../output/inv/wt/pairs/sample_inv_ref_wt.pairs
warnings.warn(UnclosedFileWarning(msg))
Traceback (most recent call last):
File "/project/venv/bin/fanc", line 127, in <module>
Fanc()
File "/project/venv/bin/fanc", line 93, in __init__
command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
File "/project/venv/lib/python3.11/site-packages/fanc/commands/fanc_commands.py", line 123, in auto
return fanc.commands.auto.auto(argv, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/project/venv/lib/python3.11/site-packages/fanc/commands/auto.py", line 1311, in auto
runner.run()
File "/project/venv/lib/python3.11/site-packages/fanc/commands/auto.py", line 141, in run
raise RuntimeError("Task {} had non-zero exit status. "
RuntimeError: Task 8aa573b9-5320-4f1b-95fa-c6c93f4fb45e had non-zero exit status. Cancelling execution of all tasks.
Some googling tells me that it's likely an incompatibility with my matplotlib and pandas versions. Could you specify versions of dependencies which have been tested and are stable?
Thank you!
The text was updated successfully, but these errors were encountered:
Hi Kau,
I'm re-running some analysis with FAN-C and created a fresh virtual environment to install into. Using
pip install fanc
I installed the package and its dependencies. Automatically, matplotlib was installed to its latest version (3.9). However, the functionregister_cmap
doesn't exist in matplotlib 3.9, so I had to manually downgrade to matplotlib 3.5.1.Now I'm running into a problem with my pandas version (currently 2.2.2). Specifically:
Some googling tells me that it's likely an incompatibility with my matplotlib and pandas versions. Could you specify versions of dependencies which have been tested and are stable?
Thank you!
The text was updated successfully, but these errors were encountered: