I'm trying to wrap my head around f2py because my organization has a lot of legacy fortran code that I would like to incorporate into some newer python-based tools I'm writing. Ideally, I would package these tools either in source packages or wheels to make it easier to distribute to the rest of the organization.
I've written a small test package based on some other examples I've seen that just sums an array of floats. The package contents are included below. If I build a source distribution tarball using py setup.py sdist, everything looks like it works. It even looks like pip successfully installs it. However, if I open a python shell and try to import the newly installed module, I get an error on the from fastadd import fadd line in the initialization script saying
AttributeError: module 'fastadd' has no attribute 'fastadd'
So it seems like it didn't actually successfully build the f2py module. Doing some troubleshooting, if I open a powershell window in the package folder and just run
py -m numpy.f2py -c fadd.pyf fadd.f90
and then open a python shell in the same folder and try to import fastadd, I get an error, ImportError: DLL load failed: The specified module could not be found. (This is after I installed the Visual Studio build tools, a fix suggested on several threads). Following the advice on this thread, changing the command to
py -m numpy.f2py -c --fcompiler=gnu95 --compiler=mingw32 fadd.pyf fadd.f90
will build a module file that I can successfully import and use. Okay, great.
However, when I change config.add_extension in the setup file to include the keyword argument f2py_options=["--fcompiler=gnu95","--compiler=mingw32"] and try to build a package distribution file with setup.py sdist command and then install using py -m pip install fastadd-1.0a1.tar.gz, I get yet a different error that says
ERROR: No .egg-info directory found in C:\Users\username\AppData\Local\Temp\pip-pip-egg-info-c7406k03
And now I'm completely flummoxed. Other configurations of the f2py_options either result in setup.py throwing an error or fail to create the extension altogether, similar to above. Using a simple string for the options gives an error, so apparently f2py_options does in fact expect a list input. I can't seem to find any good documentation on whether I'm using f2py_options correctly, and I have no idea why just adding that option would cause pip to not know where its info directory is. That makes no sense to me. I'd really appreciate some help on this one.
I'm running Python 3.7.0 32-bit, numpy 1.20.1, and pip 21.0.1 on a Windows 10 machine.
--EDIT--
Looking in the installation directory of the test module, I found a new wrinkle to this problem: the installation directory does not actually include any files listed in MANIFEST, not even the __init__.py file. If I copy __init__.py into the directory, trying to import the module gives the same ImportError: DLL load failed error I've been getting.
Also, inspecting the output of py -m pip install, it looks like numpy.distutils doesn't recognize --fcompiler or --compiler as valid options and just ignores them, even though numpy.f2py does recognize them.
--END EDIT--
PACKAGE CONTENTS:
+-fastadd
---__init__.py
---fadd.f90
---fadd.pyf
-MANIFEST.in
-README
-setup.py
fadd.f90 has the following contents:
subroutine fadd(vals,n,mysum)
integer, intent(in) :: n
real*8, intent(out):: mysum
real*8, dimension(n), intent(in) :: vals
mysum = sum(vals)
end subroutine fadd
fadd.pyf has the following contents:
python module fastadd ! in
interface ! in :fastadd
subroutine fadd(vals,n,mysum) ! in :fastadd:fadd.f90
real*8 dimension(n),intent(in) :: vals
integer, optional,intent(in),check(len(vals)>=n),depend(vals) :: n=len(vals)
real*8 intent(out) :: mysum
end subroutine fadd
end interface
end python module fastadd
__init__.py:
"""This is the documentation!"""
from .fastadd import fadd
MANIFEST.in:
include README
recursive-include fastadd *.f90
recursive-include fastadd *.pyf
recursive-include fastadd *.py
and, finally, setup.py:
def configuration(pth=None):
from numpy.distutils.misc_util import Configuration
config = Configuration(
'fastadd',
top_path=pth,
version='1.0a1',
author='John Doe',
author_email='john.doe#fake-org.biz',
url='fake-org.biz/fastadd',
description="Testing f2py build process. Sums an arbitrary-length list of numbers.")
config.add_extension(
'fastadd',
sources=['fastadd\\fadd.pyf','fastadd\\fadd.f90']
)
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration('fastadd').todict())
If it helps at all, the final MANIFEST file looks like this after the setup script is run:
# file GENERATED by distutils, do NOT edit
README
setup.py
C:\Users\username\Documents\Development\python_modules\fastadd\fastadd\fadd.f90
C:\Users\username\Documents\Development\python_modules\fastadd\fastadd\fadd.pyf
fastadd\__init__.py
fastadd\fadd.f90
fastadd\fadd.pyf
Using setuptools==27.2.0, the travis tests of our package picca (https://github.com/igmhub/picca) works well. It is no longer the case using the latest version of setuptools==41.0.0: https://github.com/igmhub/picca/issues/591 .
The issue seems to be linked to where setuptools tries to read the scripts.
I get the following error:
Traceback (most recent call last):
File "/home/travis/virtualenv/python3.6.3/bin/picca_deltas.py", line 4, in <module>
__import__('pkg_resources').run_script('picca==4.0', 'picca_deltas.py')
File "/home/travis/virtualenv/python3.6.3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/travis/virtualenv/python3.6.3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1437, in run_script
.format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/picca_deltas.py' not found in metadata at '/home/travis/build/igmhub/picca/py/picca.egg-info'
When looking to the path /home/travis/build/igmhub/picca/py/picca.egg-info/ indeed there are no scripts folder.
Our python setup is the following, is there something we should change so that setup tools know where to find the scripts?
#!/usr/bin/env python
import glob
from setuptools import setup
scripts = glob.glob('bin/*')
description = "Package for Igm Cosmological-Correlations Analyses"
version="4.0"
setup(name="picca",
version=version,
description=description,
url="https://github.com/igmhub/picca",
author="<***>",
author_email="<***>",
packages=['picca','picca.fitter2'],
package_dir = {'': 'py'},
package_data = {'picca': ['fitter2/models/*/*.fits']},
install_requires=['numpy','scipy','iminuit','healpy','fitsio',
'llvmlite','numba','h5py','future','setuptools'],
test_suite='picca.test.test_cor',
scripts = scripts
)
The command /home/travis/virtualenv/python3.6.3/bin/picca_deltas.py looks like the following on my computer:
#!<where is python>/python/3.6.3/bin/python
# EASY-INSTALL-SCRIPT: 'picca==4.0','picca_deltas.py'
__requires__ = 'picca==4.0'
__import__('pkg_resources').run_script('picca==4.0', 'picca_deltas.py')
Thanks for the help.
This is a wild shot, but I just had the same issue.
Look at how /home/travis/build/igmhub/picca/py/picca.egg-info looks like your build folder. It shouldn't be looking into the egg-info in the build folder, but the one you installed.
Just change directory and you should be fine:
cd .. # or cd anywhere outside your build folder
picca_deltas.py
Should work fine.
I found a fix, I now run the test using pytest instead of python setup.py test.
https://github.com/igmhub/picca/pull/698/files.
The clue was in the following message;
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
Why script can't find new module after using system command to install package when the script in the running status:
what directory structure looks like:
mymoduledir
|- target_module_dir
|- main.py
main.py code like this:
if __name__ == "__main__":
try:
import target_module
print("module already exist")
# to-do something
except ImportError:
print("has not target_module, start install")
os.system("cd target-module-dir && python setup.py install")
print("install finished")
import target_module
# to-do something
I found that:
if python environment has no target module, my script will auto install it successfully, but I got import error. log display:
has not target_module, start install
running install
.....
Finished processing dependencies for target_module
install finished
Traceback (most recent call last):
File ".\main.py", line 237, in
import target_module
ImportError: No module named target_module_name
It means that the target module was installed successfully, but I met an importerror when I want to import it. To prove my conclusion, I open the python shell and try import the target module, it works. When I rerun this script, log display:
module already exist
It means this script import target module successfully
What I think is:
script will check the python environment before launched, if I want to import an new module in running status of script, I need to let the script know the environment has updated.
What I have try is:
I have searched many related problem, but I haven't got an effective solution.
For some reason, I must use python2.6 to complete my function.And I try to use reload function, like this, but it can't work.
What should I do to solve this problem?
Using pip install will work well, My Solution:
import pip
if __name__ == "__main__":
try:
import target_module
print("module already exist")
# to-do something
except ImportError:
print("has not target_module, start install")
pip.main(['install', './target_module_dir/'])
print("install finished")
import target_module
# to-do something
I need to install a python module in the site packages that also will be used as a command line application. Suppose I have a module like:
app.py
def main():
print 'Dummy message'
if __name__ == '__main__':
main()
setup.py
import distutils
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
if __name__ == '__main__':
setup(name = 'dummy',
version = '1.0',
packages = ['dummy'],
)
Creating the dist by:
setup.py sdist
Install:
setup.py install
And now I would like to use it as a command line application by opening the command window and typing just: dummy
Is it possible to create such application under windows without to carry out registering system pat variables and so on ...
You can use the options in setup.py to declare command line scripts. Please refer to this article. On Windows, the script will be created in "C:\Python26\Scripts" (if you didn't change the path) - lots of tools store their scripts there (e.g. "easy_install", "hg", ...).
Put the following in dummy.cmd:
python.exe -m dummy
Or is it dummy.app...
Oh well, it's one of those.
What's a good way to check if a package is installed while within a Python script? I know it's easy from the interpreter, but I need to do it within a script.
I guess I could check if there's a directory on the system that's created during the installation, but I feel like there's a better way. I'm trying to make sure the Skype4Py package is installed, and if not I'll install it.
My ideas for accomplishing the check
check for a directory in the typical install path
try to import the package and if an exception is throw, then install package
If you mean a python script, just do something like this:
Python 3.3+ use sys.modules and find_spec:
import importlib.util
import sys
# For illustrative purposes.
name = 'itertools'
if name in sys.modules:
print(f"{name!r} already in sys.modules")
elif (spec := importlib.util.find_spec(name)) is not None:
# If you choose to perform the actual import ...
module = importlib.util.module_from_spec(spec)
sys.modules[name] = module
spec.loader.exec_module(module)
print(f"{name!r} has been imported")
else:
print(f"can't find the {name!r} module")
Python 3:
try:
import mymodule
except ImportError as e:
pass # module doesn't exist, deal with it.
Python 2:
try:
import mymodule
except ImportError, e:
pass # module doesn't exist, deal with it.
As of Python 3.3, you can use the find_spec() method
import importlib.util
# For illustrative purposes.
package_name = 'pandas'
spec = importlib.util.find_spec(package_name)
if spec is None:
print(package_name +" is not installed")
Updated answer
A better way of doing this is:
import subprocess
import sys
reqs = subprocess.check_output([sys.executable, '-m', 'pip', 'freeze'])
installed_packages = [r.decode().split('==')[0] for r in reqs.split()]
The result:
print(installed_packages)
[
"Django",
"six",
"requests",
]
Check if requests is installed:
if 'requests' in installed_packages:
# Do something
Why this way? Sometimes you have app name collisions. Importing from the app namespace doesn't give you the full picture of what's installed on the system.
Note, that proposed solution works:
When using pip to install from PyPI or from any other alternative source (like pip install http://some.site/package-name.zip or any other archive type).
When installing manually using python setup.py install.
When installing from system repositories, like sudo apt install python-requests.
Cases when it might not work:
When installing in development mode, like python setup.py develop.
When installing in development mode, like pip install -e /path/to/package/source/.
Old answer
A better way of doing this is:
import pip
installed_packages = pip.get_installed_distributions()
For pip>=10.x use:
from pip._internal.utils.misc import get_installed_distributions
Why this way? Sometimes you have app name collisions. Importing from the app namespace doesn't give you the full picture of what's installed on the system.
As a result, you get a list of pkg_resources.Distribution objects. See the following as an example:
print installed_packages
[
"Django 1.6.4 (/path-to-your-env/lib/python2.7/site-packages)",
"six 1.6.1 (/path-to-your-env/lib/python2.7/site-packages)",
"requests 2.5.0 (/path-to-your-env/lib/python2.7/site-packages)",
]
Make a list of it:
flat_installed_packages = [package.project_name for package in installed_packages]
[
"Django",
"six",
"requests",
]
Check if requests is installed:
if 'requests' in flat_installed_packages:
# Do something
If you want to have the check from the terminal, you can run
pip3 show package_name
and if nothing is returned, the package is not installed.
If perhaps you want to automate this check, so that for example you can install it if missing, you can have the following in your bash script:
pip3 show package_name 1>/dev/null #pip for Python 2
if [ $? == 0 ]; then
echo "Installed" #Replace with your actions
else
echo "Not Installed" #Replace with your actions, 'pip3 install --upgrade package_name' ?
fi
Open your command prompt type
pip3 list
As an extension of this answer:
For Python 2.*, pip show <package_name> will perform the same task.
For example pip show numpy will return the following or alike:
Name: numpy
Version: 1.11.1
Summary: NumPy: array processing for numbers, strings, records, and objects.
Home-page: http://www.numpy.org
Author: NumPy Developers
Author-email: numpy-discussion#scipy.org
License: BSD
Location: /home/***/anaconda2/lib/python2.7/site-packages
Requires:
Required-by: smop, pandas, tables, spectrum, seaborn, patsy, odo, numpy-stl, numba, nfft, netCDF4, MDAnalysis, matplotlib, h5py, GridDataFormats, dynd, datashape, Bottleneck, blaze, astropy
In the Terminal type
pip show some_package_name
Example
pip show matplotlib
You can use the pkg_resources module from setuptools. For example:
import pkg_resources
package_name = 'cool_package'
try:
cool_package_dist_info = pkg_resources.get_distribution(package_name)
except pkg_resources.DistributionNotFound:
print('{} not installed'.format(package_name))
else:
print(cool_package_dist_info)
Note that there is a difference between python module and a python package. A package can contain multiple modules and module's names might not match the package name.
if pip list | grep -q \^'PACKAGENAME\s'
# installed ...
else
# not installed ...
fi
You can use this:
class myError(exception):
pass # Or do some thing like this.
try:
import mymodule
except ImportError as e:
raise myError("error was occurred")
Method 1
to search weather a package exists or not use pip3 list command
#**pip3 list** will display all the packages and **grep** command will search for a particular package
pip3 list | grep your_package_name_here
Method 2
You can use ImportError
try:
import your_package_name
except ImportError as error:
print(error,':( not found')
Method 3
!pip install your_package_name
import your_package_name
...
...
I'd like to add some thoughts/findings of mine to this topic.
I'm writing a script that checks all requirements for a custom made program. There are many checks with python modules too.
There's a little issue with the
try:
import ..
except:
..
solution.
In my case one of the python modules called python-nmap, but you import it with import nmap and as you see the names mismatch. Therefore the test with the above solution returns a False result, and it also imports the module on hit, but maybe no need to use a lot of memory for a simple test/check.
I also found that
import pip
installed_packages = pip.get_installed_distributions()
installed_packages will have only the packages has been installed with pip.
On my system pip freeze returns over 40 python modules, while installed_packages has only 1, the one I installed manually (python-nmap).
Another solution below that I know it may not relevant to the question, but I think it's a good practice to keep the test function separate from the one that performs the install it might be useful for some.
The solution that worked for me. It based on this answer How to check if a python module exists without importing it
from imp import find_module
def checkPythonmod(mod):
try:
op = find_module(mod)
return True
except ImportError:
return False
NOTE: this solution can't find the module by the name python-nmap too, I have to use nmap instead (easy to live with) but in this case the module won't be loaded to the memory whatsoever.
I would like to comment to #ice.nicer reply but I cannot, so ...
My observations is that packages with dashes are saved with underscores, not only with dots as pointed out by #dwich comment
For example, you do pip3 install sphinx-rtd-theme, but:
importlib.util.find_spec(sphinx_rtd_theme) returns an Object
importlib.util.find_spec(sphinx-rtd-theme) returns None
importlib.util.find_spec(sphinx.rtd.theme) raises ModuleNotFoundError
Moreover, some names are totally changed.
For example, you do pip3 install pyyaml but it is saved simply as yaml
I am using python3.8
If you'd like your script to install missing packages and continue, you could do something like this (on example of 'krbV' module in 'python-krbV' package):
import pip
import sys
for m, pkg in [('krbV', 'python-krbV')]:
try:
setattr(sys.modules[__name__], m, __import__(m))
except ImportError:
pip.main(['install', pkg])
setattr(sys.modules[__name__], m, __import__(m))
A quick way is to use python command line tool.
Simply type import <your module name>
You see an error if module is missing.
$ python
Python 2.7.6 (default, Jun 22 2015, 17:58:13)
>>> import sys
>>> import jocker
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named jocker
$
Hmmm ... the closest I saw to a convenient answer was using the command line to try the import. But I prefer to even avoid that.
How about 'pip freeze | grep pkgname'? I tried it and it works well. It also shows you the version it has and whether it is installed under version control (install) or editable (develop).
I've always used pylibcheck to check if a lib is installed or not, simply download it by doing pip install pylibcheck and the could could be like this
import pylibcheck
if not pylibcheck.checkPackage("mypackage"):
#not installed
it also supports tuples and lists so you can check multiple packages and if they are installed or not
import pylibcheck
packages = ["package1", "package2", "package3"]
if pylibcheck.checkPackage(packages):
#not installed
you can also install libs with it if you want to do that, recommend you check the official pypi
The top voted solution which uses techniques like importlib.util.find_spec and sys.modules and catching import exceptions works for most packages but fails in some edge cases (such as the beautifulsoup package) where the package name used in imports is somewhat different (bs4 in this case) than the one used in setup file configuration. For these edge cases, this solution doesn't work unless you pass the package name used in imports instead of the one used in requirements.txt or pip installations.
For my use case, I needed to write a package checker that checks installed packages based on requirements.txt, so this solution didn't work. What I ended up using was subprocess.check to call the pip module explicitly to check for the package installation:
import subprocess
for pkg in packages:
try:
subprocess.check_output('py -m pip show ' + pkg)
except subprocess.CalledProcessError as ex:
not_found.append(pkg)
It's a bit slower than the other methods but more reliable and handles the edge cases.
Go option #2. If ImportError is thrown, then the package is not installed (or not in sys.path).
Is there any chance to use the snippets given below? When I run this code, it returns "module pandas is not installed"
a = "pandas"
try:
import a
print("module ",a," is installed")
except ModuleNotFoundError:
print("module ",a," is not installed")
But when I run the code given below:
try:
import pandas
print("module is installed")
except ModuleNotFoundError:
print("module is not installed")
It returns "module pandas is installed".
What is the difference between them?