I have multiple python projects which should use a number of shared files but I can not figure out how to do this in python.
If I just copy the file into the pyhton working directory it works fine with:
from HBonds import calculateHBondsForSeveralReplicas, compareSameShapeHBMatrices, calculateHBonds
But I do not want to copy it. I want to include it from: /home/b/data/pythonWorkspace/util/HBonds
For me it would make sense to do it like this (but it does not work):
from /home/b/data/pythonWorkspace/util/HBonds/HBonds.py import calculateHBondsForSeveralReplicas, compareSameShapeHBMatrices, calculateHBonds
How can I do this?
You have to make sure the PYTHONPATH includes the path to that directory as it was pointed out in previous answer.
Or you can use a nastier way: make it available at runtime with piece of code like this.
import os
import sys
folder = os.path.dirname('/home/b/data/pythonWorkspace/util/')
if dossier not in sys.path:
sys.path.append(folder)
from HBonds import HBonds
For 3rd-party libraries, it's best to install them the stock way - either to the system's site-packages or into a virtualenv.
For project(s) you're actively developing at the machine where it's running, a maintainable solution is to add their root directory(ies) to PYTHONPATH so that you can import <top_level_module>.<submodule>.<etc> from anywhere. That's what we did at my previous occupation. The main plus here is trivial code base update and switch.
Another way is to use relative imports, but it's intended for intra-package references, so that you don't have to reiterate the package's name everywhere. If many otherwise unrelated parts of the code use the same module(s), it's probably more convenient to make the shared part a separate package which would be a dependency for all of them.
Related
I am creating a Python package with multiple modules. I want to make sure that when I import modules within the package that they are importing only from the package and not something outside the package that has the same name.
Is the correct way of doing this is to use relative imports? Will this interfere when I move my package to a different location on my machine (or gets installed wherever on a customer's machine)?
Modern relative imports (here's a reference) are package-relative and package-specific, so as long as the internal structure of your package does not change you can move the package as a whole around wherever you want.
While Joran Beasley's answer should work as well (though does not seem necessary in those older versions of Python where absolute imports aren't the default, as the old style of importing checked within the package's directory first), I personally don't really like modifying the import path like that when you don't have to, especially if you need to load some of those other packages or modules that your modules or packages now shadow.
A warning, however: these do require that the module in question is loaded as part of a package, or at least have their __name__ set to indicate a location in a package. Relative imports won't work for a module when __name__ == '__main__', so if you're writing a simple/casual script that utilizes another module in the same directory as it (and want to make sure the script will refer to the proper directory, things won't work right if the current working directory is not set to the script's), you could do something like import os, sys; sys.path.insert(0, os.path.dirname(os.path.abspath(__file__))) (with thanks to https://stackoverflow.com/a/1432949/138772 for the idea). As noted in S.Lott's answer to the same question, this probably isn't something you'd want to do professionally or as part of a team project, but for something personal where you're just doing some menial task automation or the like it should be fine.
the sys.path tells python where to look for imports
add
import sys
sys.path.insert(0,".")
to the top of your main python script this will ensure local packages are imported BEFORE builtin packages (although tbh I think this happens automagically)
if you really want to import only packages in your folder do
import sys
sys.path = ["."]
however I do not recommend this at all as it will probably break lots of your stuff ...
most IDE's (eclipse/pycharm/etc) provide mechanisms to set up the environment a project uses including its paths
really the best option is not to name packages the same as builtin packages or 3rd party modules that are installed on your system
also the best option is to distribute it via a correctly bundled package, this should more than suffice
I need to ship a collection of Python programs that use multiple packages stored in a local Library directory: the goal is to avoid having users install packages before using my programs (the packages are shipped in the Library directory). What is the best way of importing the packages contained in Library?
I tried three methods, but none of them appears perfect: is there a simpler and robust method? or is one of these methods the best one can do?
In the first method, the Library folder is simply added to the library path:
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'Library'))
import package_from_Library
The Library folder is put at the beginning so that the packages shipped with my programs have priority over the same modules installed by the user (this way I am sure that they have the correct version to work with my programs). This method also works when the Library folder is not in the current directory, which is good. However, this approach has drawbacks. Each and every one of my programs adds a copy of the same path to sys.path, which is a waste. In addition, all programs must contain the same three path-modifying lines, which goes against the Don't Repeat Yourself principle.
An improvement over the above problems consists in trying to add the Library path only once, by doing it in an imported module:
# In module add_Library_path:
sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'Library'))
and then to use, in each of my programs:
import add_Library_path
import package_from_Library
This way, thanks to the caching mechanism of CPython, the module add_Library_path is only run once, and the Library path is added only once to sys.path. However, a drawback of this approach is that import add_Library_path has an invisible side effect, and that the order of the imports matters: this makes the code less legible, and more fragile. Also, this forces my distribution of programs to inlude an add_Library_path.py program that users will not use.
Python modules from Library can also be imported by making it a package (empty __init__.py file stored inside), which allows one to do:
from Library import module_from_Library
However, this breaks for packages in Library, as they might do something like from xlutils.filter import …, which breaks because xlutils is not found in sys.path. So, this method works, but only when including modules in Library, not packages.
All these methods have some drawback.
Is there a better way of shipping programs with a collection of packages (that they use) stored in a local Library directory? or is one of the methods above (method 1?) the best one can do?
PS: In my case, all the packages from Library are pure Python packages, but a more general solution that works for any operating system is best.
PPS: The goal is that the user be able to use my programs without having to install anything (beyond copying the directory I ship them regularly), like in the examples above.
PPPS: More precisely, the goal is to have the flexibility of easily updating both my collection of programs and their associated third-party packages from Library by having my users do a simple copy of a directory containing my programs and the Library folder of "hidden" third-party packages. (I do frequent updates, so I prefer not forcing the users to update their Python distribution too.)
Messing around with sys.path() leads to pain... The modern package template and Distribute contain a vast array of information and were in part set up to solve your problem.
What I would do is to set up setup.py to install all your packages to a specific site-packages location or if you could do it to the system's site-packages. In the former case, the local site-packages would then be added to the PYTHONPATH of the system/user. In the latter case, nothing needs to changes
You could use the batch file to set the python path as well. Or change the python executable to point to a shell script that contains a modified PYTHONPATH and then executes the python interpreter. The latter of course, means that you have to have access to the user's machine, which you do not. However, if your users only run scripts and do not import your own libraries, you could use your own wrapper for scripts:
#!/path/to/my/python
And the /path/to/my/python script would be something like:
#!/bin/sh
PYTHONPATH=/whatever/lib/path:$PYTHONPATH /usr/bin/python $*
I think you should have a look at path import hooks which allow to modify the behaviour of python when searching for modules.
For example you could try to do something like kde's scriptengine does for python plugins[1].
It adds a special token to sys.path(like "<plasmaXXXXXX>" with XXXXXX being a random number just to avoid name collisions) and then when python try to import modules and can't find them in the other paths, it will call your importer which can deal with it.
A simpler alternative is to have a main script used as launcher which simply adds the path to sys.path and execute the target file(so that you can safely avoid putting the sys.path.append(...) line on every file).
Yet an other alternative, that works on python2.6+, would be to install the library under the per-user site-packages directory.
[1] You can find the source code under /usr/share/kde4/apps/plasma_scriptengine_python in a linux installation with kde.
I have two Python packages where one needs to be imported by the other. The directory structure is like follows:
workspace/
management/
__init__.py
handle_management.py
other_management.py
utils/
__init__.py
utils_dict.py
I'm trying to import functionality from the utils project in the handle_management.py file:
import utils.utils_dict
Error I'm getting when trying to run handle_management.py:
ImportError: No module named utils.utils_dict
I've read a lot about how to resolve this problem and I can't seem to find a solution that works.
I started with Import a module from a relative path - I tried the applicable solutions but none worked.
Is the only solution to make workspace/ available via site_packages? If so, what is the best way to do this?
EDIT:
I've tried to add the /home/rico/workspace/ to the PYTHONPATH - no luck.
EDIT 2:
I was able to successfully use klobucar's solution but I don't think it will work as a general solution since this utility is going to be used by several other developers. I know I can use some Python generalizations to determine the relative path for each user. I just feel like there is a more elegant solution.
Ultimately this script will run via cron to execute unit testing on several Python projects. This is also going to be available to each developer to ensure integration testing during their development.
I need to be able to make this more general.
EDIT 3:
I'm sorry, but I don't really like any of these solutions for what I'm trying to accomplish. I appreciate the input - and I'm using them as a temporary fix. As a complete fix I'm going to look into adding a script available in the site_packages directory that will add to the PYTHONPATH. This is something that is needed across several machines and several developers.
Once I build my complete solution I'll post back here with what I did and mark it as a solution.
EDIT 4:
I feel as though I didn't do a good job expressing my needs with this question. The answers below addressed this question well - but not my actual needs. As a result I have restructured my question in another post. I considered editing this one, but then the answers below (which would be very helpful for others) wouldn't be meaningful to the change and would seem out of place and irrelevant.
For the revised version of this question please see Unable to import Python package universally
You have 2 solutions:
Either put workspace in your PYTHONPATH:
import sys
sys.path.append('/path/to/workspace')
from utils import utils_dict
(Note that if you're running a script inside workspace, that is importing handle_management, most probably workspace is already in your PYTHONPATH, and you wouldn't need to do that, but it seems it's not the case HERE).
Or, make "workspace" a package by adding an empty (or not) __init__.py file in the workspace directory. Then:
from ..utils import utils_dict
I would prefer the second, because you would have a problem if there's another module called "utils" in you PYTHONPATH
Apart from that, you are importing wrong here: import utils.utils_dict.py. You don't need to include the extension of the file ".py". You are not importing the file, you are importing the module (or package if it's a folder), so you don't want the path to that file, you need its name.
What you need to do is add workspace to your import path. I would make a wrapper that does this for you in workspace or just put workspace in you PYTHONPATH as an environment variable.
import sys
# Add the workspace folder path to the sys.path list
sys.path.append('/path/to/workspace/')
from workspace.utils import utils_dict
Put "workspace/" in your PYTHONPATH to make the packages underneath available to you when it searches.
This can be done from your shell profile (if you are on *nix, or environment variables on windows.
For instance, on OSX you might add to your ~/.profile (if workspace is in your home directory):
export PYTHONPATH=$HOME/workspace:$PYTHONPATH
Another option is to use virtualenv to make your project area its own contained environment.
I do a lot of work on different projects (I'm a scientist) in a fairly standardised directory structure. e.g.:
project
/analyses/
/lib
/doc
/results
/bin
I put all my various utility scripts in /bin/ because cleanliness is next to godliness. However, I have to hard code paths (e.g. ../../x/y/z) and then I have to run things within ./bin/ or they break.
I've used Django and that has /manage.py which runs various django-things and automatically handles the path. I've also used fabric to run various user defined functions.
Question: How do I do something similar? and what's the best way? I can easily write something in /manage.py to inject the root dir into sys.path etc, but then I'd like to be able to do "./manage.py foo" which would run /bin/foo.py. Or is it possible to get fabric to call executables from a certain directory?
Basically - I want something easy and low maintenance. I want to be able to drop an executable script/file/whatever into ./bin/ and not have to deal with path issues or import issues.
What is the best way to do this?
Keep Execution at TLD
In general, try to keep your runtime at top-level. This will straighten out your imports tremendously.
If you have to do a lot of import addressing with relative imports, there's probably a
better way.
Modifying The Path
Other poster's have mentioned the PYTHONPATH. That's a great way to do it permanently in your shell.
If you don't want to/aren't able to manipulate the PYTHONPATH project path directly you can use sys.path to get yourself out of relative import hell.
Using sys.path.append
sys.path is just a list internally. You can append to it to add stuff to into your path.
Say I'm in /bin and there's a library markdown in lib/. You can append a relative paths with sys.path to import what you want.
import sys
sys.path.append('../lib')
import markdown
print markdown.markdown("""
Hello world!
------------
""")
Word to the wise: Don't get too crazy with your sys.path additions. Keep your schema simple to avoid yourself a lot confusion.
Overly eager imports can sometimes lead to cases where a python module needs to import itself, at which point execution will halt!
Using Packages and __init__.py
Another great trick is creating python packages by adding __init__.py files. __init__.py gets loaded before any other modules in the directory, so it's a great way to add imports across the entire directory. This makes it an ideal spot to add sys.path hackery.
You don't even need to necessarily add anything to the file. It's sufficient to just do touch __init__.py at the console to make a directory a package.
See this SO post for a more concrete example.
In a shell script that you source (not run) in your current shell you set the following environment variables:
PATH=$PATH:$PROJECTDIR/bin
PYTHONPATH=$PROJECTDIR/lib
Then you put your Python modules and package tree in your projects ./lib directory. Python automatically adds the PYTHONPATH environment variable to sys.path.
Then you can run any top-level script from the shell without specifying the path, and any imports from your library modules are looked for in the lib directory.
I recommend very simple top-level scripts, such as:
#!/usr/bin/python
import sys
import mytool
mytool.main(sys.argv)
Then you never have to change that, you just edit the module code, and also benefit from the byte-code caching.
You can easily achieve your goals by creating a mini package that hosts each one of your projects. Use paste scripts to create a simple project skeleton. And to make it executable, just install it via setup.py develop. Now your bin scripts just need to import the entry point to this package and execute it.
What's the shortest way to import a module from a distant, relative directory?
We've been using this code which isn't too bad except your current working directory has to be the same as the directory as this code's or the relative path breaks, which can be error prone and confusing to users.
import sys
sys.path.append('../../../Path/To/Shared/Code')
This code (I think) fixes that problem but is a lot more to type.
import os,sys
sys.path.append(os.path.realpath(os.path.join(os.path.dirname(__file__), '../../../Path/To/Shared/Code')))
Is there a shorter way to append the absolute path? The brevity matters because this is going to have to be typed/appear in a lot of our files. (We can't factor it out because then it would be in the shared code and we couldn't get to it. Chicken & egg, bootstrapping, etc.)
Plus it bothers me that we keep blindly appending to sys.path but that would be even more code. I sure wish something in the standard library could help with this.
This will typically appear in script files which are run from the command line. We're running Python 2.6.2.
Edit:
The reason we're using relative paths is that we typically have multiple, independent copies of the codebase on our computers. It's important that each copy of the codebase use its own copy of the shared code. So any solution which supports only a single code base (e.g., 'Put it in site-packages.') won't work for us.
Any suggestions? Thank you!
Since you don't want to install it in site-packages, you should use buildout or virtualenv to create isolated development environments. That solves the problem, and means you don't have to fiddle with sys.path anymore (in fact, because Buildout does exactly that for you).
You've explained in a comment why you don't want to install "a single site-packages directory", but what about putting in site-packages a single, tiny module, say jebootstrap.py:
import os, sys
def relative_dir(apath):
return os.path.realpath(
os.path.join(os.path.dirname(apath),
'../../../Path/To/Shared/Code'))
def addpack(apath):
relative = relative_dir(apath)
if relative not in sys.path:
sys.path.append(relative)
Now everywhere in your code you can just have
import jebootstrap
jebootsrap.addpack(__file__)
and all the rest of your shared codebase can remain independent per-installation.
Any reason you wouldn't want to make your own shared-code dir under site-packages? Then you could just import import shared.code.module...
You have several ways to handle imports, all documented in the Python language manual.
See http://docs.python.org/library/site.html and http://docs.python.org/reference/simple_stmts.html#the-import-statement
Put it in site-packages and have multiple Python installations. You select the installation using the ordinary PATH environment variable.
Put the directory in your PYTHONPATH environment variable. This is a per-individual-person setting, so you can manage to have multiple versions of the codebase this way.
Put the directory in .pth files in your site-packages. You select the installation using the ordinary PATH environment variable.