I am trying to generate API documentation from comments (in numpydoc style) in my project and I am stuck at vague import errors from sphinx:
/home/carbolymer/workspace/si-app/doc/source/scripts.rst:10: WARNING: autodoc: failed to import module 'scripts.backtest'; the following exception was raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/carbolymer/workspace/si-app/application/scripts/backtest.py", line 6, in <module>
from scipy import stats
File "/usr/lib/python3.5/site-packages/scipy/__init__.py", line 64, in <module>
from numpy import __version__ as __numpy_version__
ImportError: cannot import name '__version__'
/home/carbolymer/workspace/si-app/doc/source/scripts.rst:18: WARNING: autodoc: failed to import module 'scripts.importdb'; the following exception was raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/site-packages/sphinx/ext/autodoc.py", line 547, in import_object
__import__(self.modname)
File "/home/carbolymer/workspace/si-app/application/scripts/importdb.py", line 5, in <module>
from si.storage.dataimport import DataImport, database_drivers, sources
File "/home/carbolymer/workspace/si-app/application/si/storage/dataimport.py", line 6, in <module>
from si.storage.datasource.file import Stooq as StooqFile
File "/home/carbolymer/workspace/si-app/application/si/storage/datasource/file.py", line 19, in <module>
from si.storage.datasource.util import correct_prices
File "/home/carbolymer/workspace/si-app/application/si/storage/datasource/util.py", line 4, in <module>
def correct_prices(dataframe, calendar=PolishCalendar()):
File "/usr/lib/python3.5/unittest/mock.py", line 917, in __call__
return _mock_self._mock_call(*args, **kwargs)
File "/usr/lib/python3.5/unittest/mock.py", line 976, in _mock_call
result = next(effect)
StopIteration
Full log:
http://pastebin.com/tycmVQdN
I've tried mocking numpy.__version__ but it does not work. Also I have no clue what about the lines containing PolishCalendar() - why sphinx is trying to mock this object?
Because of those import errors, these files are missing in the documentation. How can I fix this?
My build command:
make clean ; sphinx-apidoc -a -f -o ./source ../application ; make html
Versions:
$ sphinx-build --version
Sphinx (sphinx-build) 1.5.1
$ python --version
Python 3.5.2
source/conf.py: http://pastebin.com/VfsiX4uZ
Related
I recently did
pip install --user sphinx-toolbox
Since then i get the following error message each time i run a python script:
Error processing line 1 of /home/jody/.local/lib/python3.9/site-packages/_sphinx_jinja2_compat.pth:
Traceback (most recent call last):
File "/usr/lib/python-exec/python3.9/../../../lib/python3.9/site.py", line 169, in addpackage
exec(line)
File "<string>", line 1, in <module>
File "/home/jody/.local/lib/python3.9/site-packages/sphinx_jinja2_compat/__init__.py", line 44, in <module>
import markupsafe # noqa: E402
ModuleNotFoundError: No module named 'markupsafe'
Remainder of file ignored
After this my scripts works normally.
How can i fix this issue?
I tried to install Django Framework in Ubuntu. and i am using python 3.8. but in normal instalation, Django 1.1 had been installed. and i changed the python3 alternative to python3.8 . and usuing python3 -m pip install django. and i installed Django(v 3.3) and used it. but after the changing the alternative, the Terminal doesn't open and start.
i deleted python3.6 from my ubuntu. and the problems had been started after that.
it seems some programs in linux run in python3.6 and after deleting that,
i can't fix the problems and the Terminal windows does not open. i tried other ways (changing the gnome-terminal file, changing the alternative to default v3.6 and fix the Broken distro), but they didn't help me. i can't open Terminal, and when i ran sudo apt update i recieved this Errors:
Any idea?
File has unexpected size (1133 != 1128). Mirror sync in progress? [IP: ***.**.***.** 80]
Release file created at: Wed, 06 May 2020 19:27:45 +0000 Fetched 1,762 B in 2s (932 B/s) Traceback (most recent call last): File "/usr/lib/cnf-update-db", line 8, in <module>
from CommandNotFound.db.creator import DbCreator File "/usr/lib/python3/dist-packages/CommandNotFound/db/creator.py", line 7, in <module>
import sqlite3 File "/usr/lib/python3.6/sqlite3/__init__.py", line 23, in <module>
from sqlite3.dbapi2 import * File "/usr/lib/python3.6/sqlite3/dbapi2.py", line 23, in <module>
import datetime File "/usr/lib/python3.6/datetime.py", line 8, in <module>
import math as _math ModuleNotFoundError: No module named 'math' Error in sys.excepthook: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/apport_python_hook.py", line 63, in apport_excepthook
from apport.fileutils import likely_packaged, get_recent_crashes File "/usr/lib/python3/dist-packages/apport/__init__.py", line 5, in <module>
from apport.report import Report File "/usr/lib/python3/dist-packages/apport/report.py", line 12, in <module>
import subprocess, tempfile, os.path, re, pwd, grp, os, time, io File "/usr/lib/python3.6/subprocess.py", line 136, in <module>
import _posixsubprocess ModuleNotFoundError: No module named '_posixsubprocess'
Original exception was: Traceback (most recent call last): File "/usr/lib/cnf-update-db", line 8, in <module>
from CommandNotFound.db.creator import DbCreator File "/usr/lib/python3/dist-packages/CommandNotFound/db/creator.py", line 7, in <module>
import sqlite3 File "/usr/lib/python3.6/sqlite3/__init__.py", line 23, in <module>
from sqlite3.dbapi2 import * File "/usr/lib/python3.6/sqlite3/dbapi2.py", line 23, in <module>
import datetime File "/usr/lib/python3.6/datetime.py", line 8, in <module>
import math as _math ModuleNotFoundError: No module named 'math' Reading package lists... Done E: Failed to fetch http://dl.google.com/linux/chrome/deb/dists/stable/main/binary-amd64/Packages.gz File has unexpected size (1133 != 1128). Mirror sync in progress? [IP:
* 80] Hashes of expected file:
- Filesize:1128 [weak]
- SHA256:*
- SHA1:*
- MD5Sum:*
Release file created at: Wed, 06 May 2020 19:27:45 +0000 E: Some index files failed to download. They have been ignored, or old ones used instead. E: Problem executing scripts APT::Update::Post-Invoke-Success 'if /usr/bin/test -w /var/lib/command-not-found/ -a -e /usr/lib/cnf-update-db; then /usr/lib/cnf-update-db > /dev/null; fi' E: Sub-process returned an error code
and below result showed when i tried to run django-admin:
Traceback (most recent call last):
File "/usr/bin/django-admin", line 5, in <module>
from django.core.management import execute_from_command_line
File "/home/pytm/.local/lib/python3.6/site-packages/django/__init__.py", line 1, in <module>
from django.utils.version import get_version
File "/home/pytm/.local/lib/python3.6/site-packages/django/utils/version.py", line 1, in <module>
import datetime
File "/usr/lib/python3.6/datetime.py", line 8, in <module>
import math as _math
ModuleNotFoundError: No module named 'math'
Error in sys.excepthook:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/apport_python_hook.py", line 63, in apport_excepthook
from apport.fileutils import likely_packaged, get_recent_crashes
File "/usr/lib/python3/dist-packages/apport/__init__.py", line 5, in <module>
from apport.report import Report
File "/usr/lib/python3/dist-packages/apport/report.py", line 12, in <module>
import subprocess, tempfile, os.path, re, pwd, grp, os, time, io
File "/usr/lib/python3.6/subprocess.py", line 136, in <module>
import _posixsubprocess
ModuleNotFoundError: No module named '_posixsubprocess'
Original exception was:
Traceback (most recent call last):
File "/usr/bin/django-admin", line 5, in <module>
from django.core.management import execute_from_command_line
File "/home/pytm/.local/lib/python3.6/site-packages/django/__init__.py", line 1, in <module>
from django.utils.version import get_version
File "/home/pytm/.local/lib/python3.6/site-packages/django/utils/version.py", line 1, in <module>
import datetime
File "/usr/lib/python3.6/datetime.py", line 8, in <module>
import math as _math
ModuleNotFoundError: No module named 'math'
profiling:/home/user/Downloads/Python-3.6.10/Programs/python.gcda:Cannot open
profiling:/home/user/Downloads/Python-3.6.10/Modules/xxsubtype.gcda:Cannot open
after a few hours, i found a way to fix the problems.
First, I made a backup of all my data(I would recommend to everyone trying this). Although it worked for me, it may fail for some reason on your machine and you don't want to lose your data.
I ran the following commands to remove the old version of python3.6 without removing all the dependencies and to directly install the default version.
sudo dpkg --remove --force-depends python3.6 python3.6-minimal libpython3.6-minimal libpython3.6-stdlib
sudo apt-get install python3.6 python3.6-minimal libpython3.6-minimal libpython3.6-stdlib
I ran sudo apt-get update and sudo apt-get upgrade before rebooting my machine.
everything became ok..
I am a complete newbie to Python.
I have downloaded and installed Anaconda 3.5.2 on Windows 7, then Eclipse Photon. Installed the PyDev Plugin.
I was able to run a few simple test programs in Eclipse.
Suddenly, without installing anything I get
Error processing line 1 of C:\Anaconda3\lib\site-packages\matplotlib-2.2.2-py3.6-nspkg.pth:
Failed to import the site module
Traceback (most recent call last):
File "C:\Anaconda3\lib\site.py", line 168, in addpackage
exec(line)
File "<string>", line 1, in <module>
File "C:\Anaconda3\lib\types.py", line 171, in <module>
import functools as _functools
File "C:\Anaconda3\lib\functools.py", line 21, in <module>
from collections import namedtuple
ImportError: cannot import name 'namedtuple'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Anaconda3\lib\site.py", line 541, in <module>
main()
File "C:\Anaconda3\lib\site.py", line 523, in main
known_paths = addsitepackages(known_paths)
File "C:\Anaconda3\lib\site.py", line 320, in addsitepackages
addsitedir(sitedir, known_paths)
File "C:\Anaconda3\lib\site.py", line 207, in addsitedir
addpackage(sitedir, name, known_paths)
File "C:\Anaconda3\lib\site.py", line 178, in addpackage
import traceback
File "C:\Anaconda3\lib\traceback.py", line 5, in <module>
import linecache
File "C:\Anaconda3\lib\linecache.py", line 8, in <module>
import functools
File "C:\Anaconda3\lib\functools.py", line 21, in <module>
from collections import namedtuple
ImportError: cannot import name 'namedtuple'
even with a "Hello World" which ran before
Any ideas what could cause this?
I have found the reason:
I have added a "PyDev Package" named "collections" in the IDE. This collided with something ....
You can try a few things. Have you tried updating the package in conda? It is possible it is not up to date. Also, with Eclipse (and with most IDEs) if things that were working a moment break without any changes it is a sign you should quit the program, give it a moment to settle, and try reopening and rerunning your code. Sometimes it is the tool's fault!
I'm struggling to get PYMC3 to install correctly on windows. I've tried using the Anaconda package via conda install -c conda-forge pymc3 and in a virtualenv using only pip as per the documentation.
It seems to install ok, but fails when running an import pymc3 with the following error. Research suggests that there may be some dependencies which are getting missed.
>>> import pymc3
WARNING (theano.sandbox.cuda): The cuda backend is deprecated and will be removed in the next release (v0.10). Please switch to the gpuarray backend. You can get more information about how to switch at this URL:
https://github.com/Theano/Theano/wiki/Converting-to-the-new-gpu-back-end%28gpuarray%29
ERROR (theano.sandbox.cuda): nvcc compiler not found on $PATH. Check your nvcc installation and try again.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\__init__.py", line 8, in <module>
from .sampling import *
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\sampling.py", line 11, in <module>
from .step_methods import (NUTS, HamiltonianMC, Metropolis, BinaryMetropolis,
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\step_methods\__init__.py", line 3, in <module>
from .hmc import HamiltonianMC
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\step_methods\hmc\__init__.py", line 1, in <module>
from .hmc import HamiltonianMC
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\step_methods\hmc\hmc.py", line 7, in <module>
from .base_hmc import BaseHMC
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\step_methods\hmc\base_hmc.py", line 2, in <module>
from .trajectory import get_theano_hamiltonian_functions
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\step_methods\hmc\trajectory.py", line 3, in <module>
from pymc3.theanof import join_nonshared_inputs, gradient, CallableTensor, floatX
ImportError: cannot import name 'floatX'
I can't find much out there about this floatx package.
Seems to be a windows thing - as it installed and runs no problems on my old Ubuntu box (with anaconda).
Any help gratefully received!
EDIT: Step closer. For some reason I had the path to the nvcc compiler wrong. So if you suffer the same check that you have the full path including "\bin" in your environmnental path. If you make a change don't forget to restart.
Now I get an error:
>>> import pymc3
WARNING (theano.sandbox.cuda): The cuda backend is deprecated and will be removed in the next release (v0.10). Please switch to the gpuarray backend. You can get more information about how to switch at this URL:
https://github.com/Theano/Theano/wiki/Converting-to-the-new-gpu-back-end%28gpuarray%29
Using gpu device 0: GeForce GTX 960M (CNMeM is disabled, cuDNN not available)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\__init__.py", line 4, in <module>
from .distributions import *
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\distributions\__init__.py", line 1, in <module>
from . import timeseries
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\distributions\timeseries.py", line 1, in <module>
import theano.tensor as tt
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\__init__.py", line 116, in <module>
theano.sandbox.cuda.tests.test_driver.test_nvidia_driver1()
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\sandbox\cuda\tests\test_driver.py", line 32, in test_nvidia_driver1
profile=False)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\compile\function.py", line 326, in function
output_keys=output_keys)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\compile\pfunc.py", line 486, in pfunc
output_keys=output_keys)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\compile\function_module.py", line 1795, in orig_function
defaults)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\compile\function_module.py", line 1661, in create
input_storage=input_storage_lists, storage_map=storage_map)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\link.py", line 699, in make_thunk
storage_map=storage_map)[:3]
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\vm.py", line 1098, in make_all
self.updated_vars,
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\vm.py", line 952, in make_vm
vm = CVM(
NameError: name 'CVM' is not defined
>>>
This I fixed with the last post here: https://groups.google.com/forum/#!msg/theano-users/JoTu61_MTLk/4ZzsVyaOf2kJ. But now stuck with an error:
>>> import pymc3
Traceback (most recent call last):
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\cutils.py", line 306, in <module>
from cutils_ext.cutils_ext import * # noqa
ImportError: No module named 'cutils_ext.cutils_ext'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\cutils.py", line 317, in <module>
from cutils_ext.cutils_ext import * # noqa
ImportError: No module named 'cutils_ext.cutils_ext'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\__init__.py", line 4, in <module>
from .distributions import *
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\distributions\__init__.py", line 1, in <module>
from . import timeseries
File "C:\Users\peter\Anaconda3\lib\site-packages\pymc3\distributions\timeseries.py", line 1, in <module>
import theano.tensor as tt
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\__init__.py", line 80, in <module>
from theano.scan_module import (scan, map, reduce, foldl, foldr, clone,
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\scan_module\__init__.py", line 41, in <module>
from theano.scan_module import scan_opt
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\scan_module\scan_opt.py", line 60, in <module>
from theano import tensor, scalar
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\tensor\__init__.py", line 9, in <module>
from theano.tensor.subtensor import *
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\tensor\subtensor.py", line 26, in <module>
import theano.gof.cutils # needed to import cutils_ext
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\cutils.py", line 320, in <module>
compile_cutils()
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\cutils.py", line 285, in compile_cutils
preargs=args)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\cmodule.py", line 2313, in compile_str
return dlimport(lib_filename)
File "C:\Users\peter\Anaconda3\lib\site-packages\theano\gof\cmodule.py", line 302, in dlimport
rval = __import__(module_name, {}, {}, [module_name])
ImportError: DLL load failed: The specified procedure could not be found.
>>>
The investigation continues! Maybe it's time to bin windows and move to linux full time!
EDIT2: I switched to a python 2.7 environment and it seems to work ok. Had to install http://mingw.org/ but after that all ok.
Would be nice to get it to work in 3.6 though. Thoughts anyone?
Ok, I managed to cobble an install together.
I had no luck with the dependency management etc using conda install -c conda-forge pymc3, and I couldn't be sure if there were issues with locations/paths to compilers etc. So I did a re-install from the start.
I went for Anaconda3 (rather than 2) and it worked fine.
1) I followed the environment setup here https://github.com/philferriere/dlwin until I got to the point of installing Theano. But instead of the version suggested I installed the latest with conda install -c rdonnelly Theano suggested by https://github.com/nouiz. This is a nice solid environment set up - and i really recommend the msys tool - I hadn't used it before.
The test script in the philferriere guide are a good way to test function/performance.
2) Then I set up pymc3 using pip install pymc3 as they suggest here https://github.com/pymc-devs/pymc3. but NOT the latest version on git.
Hope someone finds this useful.
Refs:
https://github.com/Theano/Theano/issues/5348
I have python2.7 and python3.5 installed via Macports. I am trying to get neovim up and running and for this I ran
$ sudo pip2 install neovim
$ sudo pip-3.5 install neovim
Which installs the packages into different subdirs of /opt/local/Library/Frameworks/Python.framework/Versions/. Now when running Python 3.5, import neovim tries to load the 2.7 package (which fails), as I can see from the stack trace.
The full error is this:
$ python3.5 -c "import neovim"
Traceback (most recent call last):
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/msgpack_rpc/event_loop/__init__.py", line 7, in <module>
from .uv import UvEventLoop
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/msgpack_rpc/event_loop/uv.py", line 5, in <module>
import pyuv
ImportError: No module named 'pyuv'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/msgpack_rpc/event_loop/asyncio.py", line 19, in <module>
import asyncio
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/asyncio/__init__.py", line 21, in <module>
from .base_events import *
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/asyncio/base_events.py", line 18, in <module>
import concurrent.futures
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/concurrent/futures/__init__.py", line 8, in <module>
from concurrent.futures._base import (FIRST_COMPLETED,
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/concurrent/futures/_base.py", line 357
raise type(self._exception), self._exception, self._traceback
^
SyntaxError: invalid syntax
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/__init__.py", line 11, in <module>
from .msgpack_rpc import (ErrorResponse, child_session, socket_session,
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/msgpack_rpc/__init__.py", line 8, in <module>
from .event_loop import EventLoop
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/msgpack_rpc/event_loop/__init__.py", line 12, in <module>
from .asyncio import AsyncioEventLoop
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/neovim/msgpack_rpc/event_loop/asyncio.py", line 22, in <module>
import trollius as asyncio
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/trollius/__init__.py", line 21, in <module>
from .base_events import *
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/trollius/base_events.py", line 39, in <module>
from . import coroutines
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/trollius/coroutines.py", line 16, in <module>
from . import futures
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/trollius/futures.py", line 19, in <module>
from . import executor
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/trollius/executor.py", line 12, in <module>
import concurrent.futures
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/concurrent/futures/__init__.py", line 8, in <module>
from concurrent.futures._base import (FIRST_COMPLETED,
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/concurrent/futures/_base.py", line 357
raise type(self._exception), self._exception, self._traceback
^
SyntaxError: invalid syntax
What do I have to do in order for Python 2.7 and 3 to coexist peacefully on my system?
I recently had this problem as well, but it was not related to PYTHONPATH, which on my machine was unset. In my situation Python and pip were installed via MacPorts. Cleaning, self-updating MacPorts and then updating pip to the most recent version, and then running the following resolved the issue:
port select --set pip pip35