I am one of the devs of a (fairly large) C++ simulation tool. Disclaimer : I'm more of a physicist than a dev. I wrote Python bindings for that project using pybind11.
I managed to get the Python module to compile with cmake. I then managed to write a setup.py file using skbuild that does compile the Python module :
python3 setup.py sdist bdist_wheel
In _skbuild/linux-x86_64-3.9/cmake-build/lib/ (and in the tar archive dist/cytosim-0.0.0.tar.gz) there is indeed a compiled library : cytosim.cpython-39-x86_64-linux-gnu.so.
However, when I want to install the module :
pip3 install dist
I get an error :
gcc: error: src/py3/dist.c: No such file or directory
I am very confused because I do not have an directory called py3 in src.
Any pointer ? Anything I'm doing wrong ? Thanks !
The command
pip3 install dist
tries (and fails) to install the dist package from the pypi repository.
Maybe try
pip3 install dist/cytosim-0.0.0.tar.gz
instead.
Related
I have successfully built a Python package that uses CMake combined with pybind11 to create a shared object (.so - assuming only Linux usage at the moment) file. The implementation works but I am unable to remove this shared object file using pip uninstall .
My setup command in setup.py file looks like this taken from the pybind/cmake_example repository:
setup(
name='package',
version='0.0.1',
author='-',
author_email='-',
description='A test project using pybind11 and CMake',
long_description='',
ext_modules=[CMakeExtension('packagebindings')],
cmdclass=dict(build_ext=CMakeBuild),
zip_safe=False,
packages=setuptools.find_packages()
)
My CMakeLists.txt file has an install instruction that looks like this:
install(TARGETS packagebindings COMPONENT python LIBRARY DESTINATION ${Python_SITELIB})
To summarise, here are the files that are created when running pip install .:
path/to/site-packages/package/* - removed by pip uninstall package
path/to/site-packages/package-0.0.1.dist-info/* - removed by pip uninstall package
path/to/site-packages/packagebindings.cpython-37m-x86_64-linux-gnu.so - still present after pip uninstall package
I would like to know how make it so that running pip uninstall . removes the .so file.
If a further MRE is required, I can link to a repository.
Your CMake install target seems to place the .so directly into the python installation directory (DESTINATION ${Python_SITE_LIB}). I'm guessing this stops the .so from being registered by Python proper, so it is not removed when uninstalling. I would suggest to make CMake place the .so in a distribution directory, and then add the following option to setup():
data_files = [("installation_bin", ["distribution_bin/library.so"])]
This will let the .so be tracked by the Python package manager. The first string is a directory relative to the installation prefix. The second string is the .so file in your distribution, relative to the setup.py script.
I am trying to install pyjnius, & when i execute simple program it shows following error..
How do i solve it?
SystemError: Error calling dlopen(/usr/lib/jvm/java-7-openjdk/jre/lib/amd64 /server/libjvm.so: /usr/lib/jvm/java-7-openjdk/jre/lib/amd6h file or directory
Pyjnius depends on Cython and Java. Assuming that you already have Java installed. Please do the following:
su
pip install cython
pip install pyjnius
Example
I am trying to export a GeoTiff with Blender using the Blender Python API (based on Python 3), so I've decided to install GDAL on Ubuntu (14.04). What I would like is to get the module as a standalone folder that I could put in the modules directory of Blender (/home/user/.config/blender/2.73/scripts/modules).
The thing is I've run through several different problems trying to install GDAL. I've tried to install from source (for GDAL 2.0.0) here : Official PyPi Gdal
I ran sudo apt-get install libgdal-dev gdal-bin (I list it here because it may be important)
When I am in the extracted GDAL folder, using python setup.py build & python setup.py install, the library installs to /usr/local/lib/python2.7/dist-packages/osgeo. However, when I run python from command line, running from osgeo import osr returns ImportError: No module named _gdal
Following GDAL via pip , I used pip (pip install GDAL) to install the library, and the folder it went to was /usr/lib/python3/dist-packages/osgeo (using pip show ...). Again, running python3 and trying to import results in the same error. Of course, when I copy-paste each folder in the blender module directory, I get the same error in the Blender Python console.
So I decided to compile the sources using ./configure --with-python & make & make install in the source folder. I then copied the folder GDAL-x.x.x/build/lib.linux-x86_64-3.4/osgeo to the blender modules directory and got this time the error when importing : ImportError: /home/yvesu/.config/blender/2.73/scripts/modules/osgeo/_gdal.so: undefined symbol: _Py_ZeroStruct.
Trying to compile with python3 using python3 setup.py build returns the error error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
EDIT 1:
I think I've found the solution : I went to the directory swig/python (not found in a GDAL-1.11.0 folder but gdal-1.11.0 fodler, can't remember where I downloaded it from), ran python3 setup.py build & python3 setup.py install and could finally find the folder in /usr/local/lib/python3.4/dist-packages/GDAL-1.11.0-py3.4-linux-x86_64.egg/osgeo. When I put this osgeo folder oni the Blender modules directory, I was able to import osgeo in Blender. I will report if anything went wrong.
I think I've listed all my attempts at installing GDAL on Ubuntu. Can anyone point me in the right direction? Do you think it is even possible to install it as a standalone module, or do I need linked libraries through LD_LIBRARY_PATH?
Here is the solution I've found :
Download Gdal sources (v2.0.0 is the current stable release) from ftp://ftp.remotesensing.org/gdal/2.0.0/ or http://download.osgeo.org/gdal/2.0.0/ and untar
Go to the directory gdal2.0.0/swig/python
Run python3 setup.py build & python3 setup.py install
Finally find the module folder in, on Ubuntu : /usr/local/lib/python3.4/dist-packages/GDAL-2.0.0-py3.4-linux-x86_64.egg/osgeo
I can now use it in Blender (copying in the modules directory)
When I try to install python-asurv using setup.py, (typing "path"\python "path"\setup.py install in the command prompt), I get the following error:
building extension "twokm" sources target build\src.win32-2.7\twokmmodule.c does not exist: Assuming twokmmodule.c was generated with "build_src --inplace" command. error: '.\\twokmmodule.c' missing`
I am on windows 7 64bit with 32bit python2.7
In the zip file that I downloaded, there is setup.py, asurv.py, asurv.pyc, two licences, a readme, and twokm.pyf and twokm.f, which I think are in fortran format (don't know anything about fortran). The README just says type python setup.py install.
I think that for the twokm.pyf and twokm.f files I need to use f2py to convert them to .py files, am I right?
How can I install python-asurv?
Make sure you have installed numpy at it is dependency of python-asurv
Do pip install numpy and then Do python setup.py install in the directory you have downloaded.
I am trying to build a Python library Healpy. My first try was to use pip. After typing:
>pip install --user healpy
i got result:
>checking if library 'cfitsio' is installed
>error: No such file or directory
After that i tried to build library on my own - i downloded the sources and builded cfitsio using commands:
>/.configure
>make
>make install
after doing that i got a libcfitsio.a file, pkg-config folder with .pc file and some .h files in include folder. But after typing:
> python setup.py install
i got the same error. I got the same error after building lib in Windows. Did anyone have similar problem ? I would be very greateful for any suggestions.
As mentioned in the healpy INSTALL documentation you must specify the PKG_CONFIG_PATH environment variable if you want to use external cfitsio or healpix modules:
PKG_CONFIG_PATH=/path/to/local/lib/pkgconfig
Note: adapt with your own path obtain from the cfitsio compilation process!
Then you shall be able to run the compilation of healpy...