Hidden Markov Models (HMM) in Python - python

I am working with Hidden Markov Models in Python. For that I came across a package/module named hmmpytk. The problem is hmmpytk isnt pre-installed and when I download the hmmpytk module, i only get codes without the installation file. I use windows operating system. If I run a code simply with "from hmmpytk import hmm_faster" I get an Import error. ..so no idea how i get started with hmmpytk.

You need to make sure that the folder hmmpytk (and possibly also lame_tagger) is "in the directory containing the script that was used to invoke the Python interpreter." See the documentation about the Python path sys.path
EDIT: Alternatively, you can make sure that those folders are on your Python path. To see the folders in your path, type import sys; sys.path - the CWD is the first entry in the path if you started the interactive interpreter.

You probably want PIP or easy_install to install python packages.

Related

Incorrect module path in Python

I recently had a problem with importing a python and therefore posted this question: Cant seem to import specific module in Python
Based on input I got I did some digging and saw the following:
If I open cygwin and input python --version, I get this
Marc#Marc ~
$ python --version
Python 2.7.12 :: Anaconda 4.2.0 (64-bit)
And if I open python using myCharm and input this:
import sys
print('\n'.join(sys.path))
I get:
C:\Users\Marc\Anaconda3\python.exe C:/Users/Marc/PycharmProjects/clustering/testing.py
C:\Users\Marc\PycharmProjects\clustering
C:\Users\Marc\PycharmProjects\clustering
C:\Users\Marc\Anaconda3\python35.zip
C:\Users\Marc\Anaconda3\DLLs
C:\Users\Marc\Anaconda3\lib
C:\Users\Marc\Anaconda3
C:\Users\Marc\Anaconda3\lib\site-packages
C:\Users\Marc\Anaconda3\lib\site-packages\Sphinx-1.4.6-py3.5.egg
C:\Users\Marc\Anaconda3\lib\site-packages\win32
C:\Users\Marc\Anaconda3\lib\site-packages\win32\lib
C:\Users\Marc\Anaconda3\lib\site-packages\Pythonwin
C:\Users\Marc\Anaconda3\lib\site-packages\setuptools-27.2.0-py3.5.egg
So assume this highlights the problem. Could anybody tell me what is wise to do here? Change the path in my terminal of change the path in python
If you set an envirnment variable called PYTHONPATH to a colon-separated (Windows: semicolon-separated) list of directories, each of them will be added to the interpreter's sys.path. This is the recommended way of making modules available.
So for example, let's suppose you had added Python modules in the directory C:\Documents and Settings\frits\private. Before you run your Python program you would execute the command
SET PYTHONPATH=C:\Documents and Settings\frits\private
No semicolon is required in this case because there's only one directory.
The when you run Python you will find that your sys.path has another entry corresponding to the C:\Documents and Settings\frits\private directory.
In the longer term, to avoid conflicts between the requirements of different projects (e.g. you want to run two programs that require a different version of the same third-party module) you should investigate the use of virtual environments.

What should I set my pythonpath to

I downloaded a python module from online and want to use it in IDLE, but I keep getting an error message saying it's not found.
My python path is "/Library/Frameworks/Python.framework/Versions/2.7/bin". If I want to be able to run modules I downloaded from online into IDLE, what should I set my python path to to be able to do that?
I am running OsX 10.10.5
Create a directory somewhere under your home directory. Let's say it's ~/pylib. Copy the module to ~/pylib. Before running IDLE execute the command
export PYTHONPATH=~/pylib
You should now be able to import the module.
If a module you have downloaded was properly packaged, it should come with the installation routine. Conventionally, it is called setup.py. If you see this file, you can just do
python setup.py install
That should take care of most packages available online and you don't even need to figure out where it was installed to.
If you really need to check/set the paths, you can check the directories as reported by
import sys
sys.prefix
sys.exec_prefix
These are the paths that point to the directories where stuff is installed (prefix/lib).
If you are looking into custom or user installation (using --user flag), check this folder: userbase/lib/python<VERSION>/site-packages
More details in the documentation.

Python cannot find module even when path is appended to sys.path

Having some weird troubles installing python modules on my work computer (read: no admin/root rights), I'm using 2.7.5. I downloaded and unpacked the tarball and ran 'setup.py', but it had no effect: When I open the python shell, it can't find the module (this specific one is fuzzywuzzy). However, if I right click -> edit with IDLE the setup.py, and then run the shell from that file, it loads and works perfectly fine. Or, if I then open a new file from that shell, use the module and run it, it works fine. -__-
I've tried using:
import sys
sys.path.append('path here')
to append the location where the module is installed, but this doesn't help, nor does the path stay in the sys.path list when I close/reopen the shell.
This is actually driving me insane. Can anyone help? I'm relatively new to programming and python.
The best and easy way provided by python to install/uninstall packages is to use PIP.
use this
python -m pip install packagename==version
same way to uninstall
python -m pip uninstall packagename==version
if you are using windows you need to set path variable first usually python file will be in path C:\Python27 to set path variable
PATH=%PATH%;C:\Python27;

python beginner: import mysite.manage fails?

Disclaimer: I am new to python and django but have Drupal programming experience. I'm using Windows 7 (same issues on Windows XP)
On python 2.7 and Django-1.3.1, I successfully created a default project
django-admin.py startproject djsite
Now, I need to "bootstrap" djsite.manage as explained here (http://www.pyinstaller.org/wiki/Recipe/DjangoApplication) in a file called bootstrap.py located in djsite's parent directory as follows:
import djsite.manage
djsite.manage.execute_manager(djsite.manage.settings,['manage.py', 'runserver'])
Yet, as soon as the compiler sees:
import djsite.manage
I get this:
"Error: Can't find the file 'settings.py' in the directory containing 'C:\Python27\Lib\site-packages\djsite\manage.pyc'. It appears you've customized things... You'll have to run django-admin.py, passing it your settings module." And, I don't know how to follow the error's advice in this situation.
However, if I instead issue the following in bootstrap.py:
import os, sys
sys.path.append(os.path.abspath('djsite'))
import djsite.manage
djsite.manage.execute_manager(djsite.manage.settings,['manage.py', 'runserver'])
the script works correctly, but it breaks Pyinstaller (I've already asked this question on that software's mailing list (http://groups.google.com/group/pyinstaller/browse_thread/thread/174a72e26c26a44c). Even if I add the path to the djsite in my PATH variable, I get the same error.
So my question here is this: Why does importing the manage.py module fail with this approach and how can I proceed? Thanks!
Try adding this to your bootstrap.py to inform it where your settings file lives:
import os
os.environ['DJANGO_SETTINGS_MODULE'] = 'djsite.settings'
This will assume that djsite is in your pythonpath. That is, if its located here: /path/to/my/djsite, then this should be in your pythonpath: /path/to/my
Actually the best way to be doing this from the start is to being using virtualenv which will ensure that your environment is correct. I feel like that had to have been part of your tutorial if I remember bootstrap at all. If you are using virtualenv, make sure you remembered to source bin/activate
If that doesn't work, you can try altering the runserver command:
args = ['manage.py', 'runserver', '--settings=/path/to/my/djsite/settings.py']
djsite.manage.execute_manager(djsite.manage.settings, args)

Python error "ImportError: No module named"

Python is installed in a local directory.
My directory tree looks like this:
(local directory)/site-packages/toolkit/interface.py
My code is in here:
(local directory)/site-packages/toolkit/examples/mountain.py
To run the example, I write python mountain.py, and in the code I have:
from toolkit.interface import interface
And I get the error:
Traceback (most recent call last):
File "mountain.py", line 28, in ?
from toolkit.interface import interface
ImportError: No module named toolkit.interface
I have already checked sys.path and there I have the directory /site-packages. Also, I have the file __init__.py.bin in the toolkit folder to indicate to Python that this is a package. I also have a __init__.py.bin in the examples directory.
I do not know why Python cannot find the file when it is in sys.path. Any ideas? Can it be a permissions problem? Do I need some execution permission?
Based on your comments to orip's post, I guess this is what happened:
You edited __init__.py on windows.
The windows editor added something non-printing, perhaps a carriage-return (end-of-line in Windows is CR/LF; in unix it is LF only), or perhaps a CTRL-Z (windows end-of-file).
You used WinSCP to copy the file to your unix box.
WinSCP thought: "This has something that's not basic text; I'll put a .bin extension to indicate binary data."
The missing __init__.py (now called __init__.py.bin) means python doesn't understand toolkit as a package.
You create __init__.py in the appropriate directory and everything works... ?
Does
(local directory)/site-packages/toolkit
have a __init__.py?
To make import walk through your directories every directory must have a __init__.py file.
I ran into something very similar when I did this exercise in LPTHW; I could never get Python to recognise that I had files in the directory I was calling from. But I was able to get it to work in the end. What I did, and what I recommend, is to try this:
(NOTE: From your initial post, I am assuming you are using an *NIX-based machine and are running things from the command line, so this advice is tailored to that. Since I run Ubuntu, this is what I did)
Change directory (cd) to the directory above the directory where your files are. In this case, you're trying to run the mountain.py file, and trying to call the toolkit.interface.py module, which are in separate directories. In this case, you would go to the directory that contains paths to both those files (or in other words, the closest directory that the paths of both those files share). Which in this case is the toolkit directory.
When you are in the toolkit directory, enter this line of code on your command line:
export PYTHONPATH=.
This sets your PYTHONPATH to ".", which basically means that your PYTHONPATH will now look for any called files within the directory you are currently in, (and more to the point, in the sub-directory branches of the directory you are in. So it doesn't just look in your current directory, but in all the directories that are in your current directory).
After you've set your PYTHONPATH in the step above, run your module from your current directory (the toolkit directory). Python should now find and load the modules you specified.
On *nix, also make sure that PYTHONPATH is configured correctly, especially that it has this format:
.:/usr/local/lib/python
(Mind the .: at the beginning, so that it can search on the current directory, too.)
It may also be in other locations, depending on the version:
.:/usr/lib/python
.:/usr/lib/python2.6
.:/usr/lib/python2.7 and etc.
You are reading this answer says that your __init__.py is in the right place, you have installed all the dependencies and you are still getting the ImportError.
I was facing a similar issue except that my program would run fine when ran using PyCharm but the above error when I would run it from the terminal. After digging further, I found out that PYTHONPATH didn't have the entry for the project directory. So, I set PYTHONPATH per Import statement works on PyCharm but not from terminal:
export PYTHONPATH=$PYTHONPATH:`pwd` (OR your project root directory)
There's another way to do this using sys.path as:
import sys
sys.path.insert(0,'<project directory>') OR
sys.path.append('<project directory>')
You can use insert/append based on the order in which you want your project to be searched.
Using PyCharm (part of the JetBrains suite) you need to define your script directory as Source:
Right Click > Mark Directory as > Sources Root
For me, it was something really stupid. I installed the library using pip3 install but was running my program as python program.py as opposed to python3 program.py.
I solved my own problem, and I will write a summary of the things that were wrong and the solution:
The file needs to be called exactly __init__.py. If the extension is different such as in my case .py.bin then Python cannot move through the directories and then it cannot find the modules. To edit the files you need to use a Linux editor, such as vi or nano. If you use a Windows editor this will write some hidden characters.
Another problem that was affecting it was that I had another Python version installed by the root, so if someone is working with a local installation of python, be sure that the Python installation that is running the programs is the local Python. To check this, just do which python, and see if the executable is the one that is in your local directory. If not, change the path, but be sure that the local Python directory is before than the other Python.
To mark a directory as a package you need a file named __init__.py, does this help?
an easy solution is to install the module using python -m pip install <library-name> instead of pip install <library-name>
you may use sudo in case of admin restrictions
To all those who still have this issue. I believe Pycharm gets confused with imports. For me, when i write 'from namespace import something', the previous line gets underlined in red, signaling that there is an error, but works. However ''from .namespace import something' doesn't get underlined, but also doesn't work.
Try
try:
from namespace import something
except NameError:
from .namespace import something
Yup. You need the directory to contain the __init__.py file, which is the file that initializes the package. Here, have a look at this.
The __init__.py files are required to make Python treat the directories as containing packages; this is done to prevent directories with a common name, such as string, from unintentionally hiding valid modules that occur later on the module search path. In the simplest case, __init__.py can just be an empty file, but it can also execute initialization code for the package or set the __all__ variable, described later.
If you have tried all methods provided above but failed, maybe your module has the same name as a built-in module. Or, a module with the same name existing in a folder that has a high priority in sys.path than your module's.
To debug, say your from foo.bar import baz complaints ImportError: No module named bar. Changing to import foo; print foo, which will show the path of foo. Is it what you expect?
If not, Either rename foo or use absolute imports.
You must have the file __ init__.py in the same directory where it's the file that you are importing.
You can not try to import a file that has the same name and be a file from 2 folders configured on the PYTHONPATH.
eg:
/etc/environment
PYTHONPATH=$PYTHONPATH:/opt/folder1:/opt/folder2
/opt/folder1/foo
/opt/folder2/foo
And, if you are trying to import foo file, python will not know which one you want.
from foo import ... >>> importerror: no module named foo
My two cents:
Spit:
Traceback (most recent call last):
File "bash\bash.py", line 454, in main
import bosh
File "Wrye Bash Launcher.pyw", line 63, in load_module
mod = imp.load_source(fullname,filename+ext,fp)
File "bash\bosh.py", line 69, in <module>
from game.oblivion.RecordGroups import MobWorlds, MobDials, MobICells, \
ImportError: No module named RecordGroups
This confused the hell out of me - went through posts and posts suggesting ugly syspath hacks (as you see my __init__.py were all there). Well turns out that game/oblivion.py and game/oblivion was confusing python
which spit out the rather unhelpful "No module named RecordGroups". I'd be interested in a workaround and/or links documenting this (same name) behavior -> EDIT (2017.01.24) - have a look at What If I Have a Module and a Package With The Same Name? Interestingly normally packages take precedence but apparently our launcher violates this.
EDIT (2015.01.17): I did not mention we use a custom launcher dissected here.
Fixed my issue by writing print (sys.path) and found out that python was using out of date packages despite a clean install. Deleting these made python automatically use the correct packages.
In my case, because I'm using PyCharm and PyCharm create a 'venv' for every project in project folder, but it is only a mini env of python. Although you have installed the libraries you need in Python, but in your custom project 'venv', it is not available. This is the real reason of 'ImportError: No module named xxxxxx' occurred in PyCharm.
To resolve this issue, you must add libraries to your project custom env by these steps:
In PyCharm, from menu 'File'->Settings
In Settings dialog, Project: XXXProject->Project Interpreter
Click "Add" button, it will show you 'Available Packages' dialog
Search your library, click 'Install Package'
Then, all you needed package will be installed in you project custom 'venv' folder.
Enjoy.
Linux: Imported modules are located in /usr/local/lib/python2.7/dist-packages
If you're using a module compiled in C, don't forget to chmod the .so file after sudo setup.py install.
sudo chmod 755 /usr/local/lib/python2.7/dist-packages/*.so
In my case, the problem was I was linking to debug python & boost::Python, which requires that the extension be FooLib_d.pyd, not just FooLib.pyd; renaming the file or updating CMakeLists.txt properties fixed the error.
My problem was that I added the directory with the __init__.py file to PYTHONPATH, when actually I needed to add its parent directory.
For me, running the file as a module helped.
Instead of
python myapp/app.py
using
python -m myapp.app
It's not exactly the same but it might be a better approach in some cases.
If you are using a setup script/utility (e.g. setuptools) to deploy your package, don't forget to add the respective files/modules to the installer.
When supported, use find_packages() or similar to automatically add new packages to the setup script. This will absolutely save you from a headache, especially if you put your project aside for some time and then add something later on.
import setuptools
setuptools.setup(
name="example-pkg",
version="0.0.1",
author="Example Author",
author_email="author#example.com",
description="A small example package",
packages=setuptools.find_packages(),
classifiers=[
"Programming Language :: Python :: 3",
"Operating System :: OS Independent",
],
python_requires='>=3.6',
)
(Example taken from setuptools documentation)
I had the same problem (Python 2.7 Linux), I have found the solution and i would like to share it. In my case i had the structure below:
Booklet
-> __init__.py
-> Booklet.py
-> Question.py
default
-> __init_.py
-> main.py
In 'main.py' I had tried unsuccessfully all the combinations bellow:
from Booklet import Question
from Question import Question
from Booklet.Question import Question
from Booklet.Question import *
import Booklet.Question
# and many othet various combinations ...
The solution was much more simple than I thought. I renamed the folder "Booklet" into "booklet" and that's it. Now Python can import the class Question normally by using in 'main.py' the code:
from booklet.Booklet import Booklet
from booklet.Question import Question
from booklet.Question import AnotherClass
From this I can conclude that Package-Names (folders) like 'booklet' must start from lower-case, else Python confuses it with Class names and Filenames.
Apparently, this was not your problem, but John Fouhy's answer is very good and this thread has almost anything that can cause this issue. So, this is one more thing and I hope that maybe this could help others.
In linux server try dos2unix script_name
(remove all (if there is any) pyc files with command find . -name '*.pyc' -delete)
and re run in the case if you worked on script on windows
In my case, I was using sys.path.insert() to import a local module and was getting module not found from a different library. I had to put sys.path.insert() below the imports that reported module not found. I guess the best practice is to put sys.path.insert() at the bottom of your imports.
I've found that changing the name (via GUI) of aliased folders (Mac) can cause issues with loading modules. If the original folder name is changed, remake the symbolic link. I'm unsure how prevalent this behavior may be, but it was frustrating to debug.
another cause makes this issue
file.py
#!/bin/python
from bs4 import BeautifulSoup
if your default python is pyyhon2
$ file $(which python)
/sbin/python: symbolic link to python2
file.py need python3, for this case(bs4)
you can not execute this module with python2 like this:
$ python file.py
# or
$ file.py
# or
$ file.py # if locate in $PATH
Tow way to fix this error,
# should be to make python3 as default by symlink
$ rm $(which python) && ln -s $(which python3) /usr/bin/python
# or use alias
alias python='/usr/bin.../python3'
or change shebang in file.py to
#!/usr/bin/...python3
After just suffering the same issue I found my resolution was to delete all pyc files from my project, it seems like these cached files were somehow causing this error.
Easiest way I found to do this was to navigate to my project folder in Windows explorer and searching for *.pyc, then selecting all (Ctrl+A) and deleting them (Ctrl+X).
Its possible I could have resolved my issues by just deleting the specific pyc file but I never tried this
I faced the same problem: Import error. In addition the library've been installed 100% correctly. The source of the problem was that on my PC 3 version of python (anaconda packet) have been installed). This is why the library was installed no to the right place. After that I just changed to the proper version of python in the my IDE PyCharm.
I had the same error. It was caused by somebody creating a folder in the same folder as my script, the name of which conflicted with a module I was importing from elsewhere. Instead of importing the external module, it looked inside this folder which obviously didn't contain the expected modules.

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