pyms error about mountainsort HOT 16 OPEN

Would you please explain step by step how you installed mountainsort?

from mountainsort.

Thanks for the reply.
Yes, I followed the instructions on https://mountainsort.readthedocs.io/en/latest/ to install with apt-get, and there didn't seem to be any issues with the main installation.
I did encounter an issue with using pip3, so did "sudo apt-get install python3-numpy" instead - could this be causing the problem?

from mountainsort.

This is the old version of mountainsort that is not currently supported. Please follow instructions on the following page: https://github.com/flatironinstitute/mountainsort_examples/blob/master/README.md

from mountainsort.

Yeah, I actually need the old version. Do you know what the issue could be?

from mountainsort.

What happens if you run /opt/mountainlab/packages/pyms/basic/basic.mp spec?

from mountainsort.

I get this message:
Traceback (most recent call last):
File "/opt/mountainlab/packages/pyms/basic/basic.py", line 7, in
from mlpy import ProcessorManager
File "/opt/mountainlab/packages/pyms/mlpy/init.py", line 2, in
from .processormanager import ProcessorManager
File "/opt/mountainlab/packages/pyms/mlpy/processormanager.py", line 4, in
from numpydoc import docscrape
File "/usr/lib/python3/dist-packages/numpydoc/init.py", line 3, in
from .numpydoc import setup
File "/usr/lib/python3/dist-packages/numpydoc/numpydoc.py", line 29, in
from sphinx.util.compat import Directive
File "/usr/lib/python3/dist-packages/sphinx/util/compat.py", line 14, in
from docutils.parsers.rst import Directive # noqa
File "/usr/lib/python3/dist-packages/docutils/parsers/rst/init.py", line 75, in
from docutils.parsers.rst import states
File "/usr/lib/python3/dist-packages/docutils/parsers/rst/states.py", line 116, in
from docutils.parsers.rst import directives, languages, tableparser, roles
File "/usr/lib/python3/dist-packages/docutils/parsers/rst/roles.py", line 78, in
from docutils.utils.code_analyzer import Lexer, LexerError
File "/usr/lib/python3/dist-packages/docutils/utils/code_analyzer.py", line 13, in
from pygments.lexers import get_lexer_by_name
File "/usr/lib/python3/dist-packages/pygments/lexers/init.py", line 20, in
from pygments.plugin import find_plugin_lexers
File "/usr/lib/python3/dist-packages/pygments/plugin.py", line 39, in
import pkg_resources
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2927, in
@_call_aside
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2913, in _call_aside
f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2952, in _initialize_master_working_set
add_activation_listener(lambda dist: dist.activate())
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 956, in subscribe
callback(dist)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2952, in
add_activation_listener(lambda dist: dist.activate())
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2515, in activate
declare_namespace(pkg)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2097, in declare_namespace
_handle_ns(packageName, path_item)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2047, in _handle_ns
_rebuild_mod_path(path, packageName, module)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2066, in _rebuild_mod_path
orig_path.sort(key=position_in_sys_path)
AttributeError: '_NamespacePath' object has no attribute 'sort'

from mountainsort.

Indeed it looks like a problem with your python installation.

Try running pip3 install --upgrade setuptools and reinstall numpy using pip3. If you have problems with that, post your errors.

from mountainsort.

Okay, yeah, thought it could be that. pip3 isn't working at all - I get this error when I run 'pip3 install --upgrade setuptools':

Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pip/_vendor/init.py", line 33, in vendored
import(vendored_name, globals(), locals(), level=0)
ImportError: No module named 'pip._vendor.pkg_resources'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/bin/pip3", line 9, in
from pip import main
File "/usr/lib/python3/dist-packages/pip/init.py", line 13, in
from pip.exceptions import InstallationError, CommandError, PipError
File "/usr/lib/python3/dist-packages/pip/exceptions.py", line 6, in
from pip._vendor.six import iteritems
File "/usr/lib/python3/dist-packages/pip/_vendor/init.py", line 75, in
vendored("pkg_resources")
File "/usr/lib/python3/dist-packages/pip/_vendor/init.py", line 36, in vendored
import(modulename, globals(), locals(), level=0)
File "", line 969, in _find_and_load
File "", line 958, in _find_and_load_unlocked
File "", line 664, in _load_unlocked
File "", line 634, in _load_backward_compatible
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2927, in
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2913, in _call_aside
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2952, in _initialize_master_working_set
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 956, in subscribe
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2952, in
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2515, in activate
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2097, in declare_namespace
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2047, in _handle_ns
File "/usr/share/python-wheels/pkg_resources-0.0.0-py2.py3-none-any.whl/pkg_resources/init.py", line 2066, in _rebuild_mod_path
AttributeError: '_NamespacePath' object has no attribute 'sort'

from mountainsort.

You do have python3-pip and python3-setuptools installed, right?

Also, are you using a regular Python installation (apt install ...) or do you have some conda environment installed?

from mountainsort.

Yes, both installed, and I installed python3 using apt install python3. I did also have python installed through conda, but tried removing it and am still getting this issue.

from mountainsort.

Conda tends to break the default installation but if you had that issue before then it shouldn't matter. Maybe try setting up a virtualenv and perform the installation there.

Something along the lines of:

python3 -m venv .mlenv
. .mlenv/bin/activate
pip install ...
ml-list-processors

from mountainsort.

Okay, thanks, will give that a go. Should I re-install everything in the venv or just numpy?

from mountainsort.

venv gives you a clean python setup so you need to install everything. Best to simply repeat MountainSort installation while in the virtual env.

from mountainsort.

Just tried re-installing within the venv and still getting the original pyms error when I type mp-list-processors.

from mountainsort.

Well, the internet claims pip install --upgrade pip and pip install --upgrade setuptools should fix your issue (you might need to replace with pip3) so you can try that (so upgrade pip first and then setuptools). What you are dealing with is unrelated to MountainSort itself but rather to your Python installation. If all elses fail, you might want to try a newer Ubuntu version or at least a newer Python installation.

But in the end you should probably switch to more recent MountainSort release.

from mountainsort.

Okay, thank you for your help - it's good to know it is most likely that. I will try and find a solution.

from mountainsort.