I am trying to create a yocto recipe for scikit-learn package. It depends on scipy pacakge. I was able to successfully build the scipy package using : https://github.com/gpanders/meta-scipy.
When I run bitbake python3-scikit-learn, i am getting the below error:
ModuleNotFoundError: No module named 'scipy'
I am executing the commands in the below order.
Once I have cloned/copied the scipy recipes and the patches listed in the meta-scipy, i am running bitbake python3-scipy and the build was successful.
Then, I created a recipe file with the name python3-scikit-learn_0.23.2.bb and the contents are as below.
PYPI_PACKAGE = "scikit-learn"
LICENSE = "BSD"
LIC_FILES_CHKSUM = "file://PKG-INFO;beginline=8;endline=8;md5=40ee42dc5a49f1617c5c78f16c50e065"
SRC_URI[sha256sum] = "20766f515e6cd6f954554387dfae705d93c7b544ec0e6c6a5d8e006f6f7ef480"
inherit pypi setuptools3
#DEPENDS = "${PYTHON_PN}-numpy-native ${PYTHON_PN}-numpy ${PYTHON_PN}-scipy ${PYTHON_PN}-joblib ${PYTHON_PN}"
DEPENDS = "${PYTHON_PN}-numpy-native ${PYTHON_PN}-numpy ${PYTHON_PN}-scipy ${PYTHON_PN}"
RDEPENDS_${PN} += "${PYTHON_PN}-numpy ${PYTHON_PN}-scipy"
When I run the bitbake python3-scikit-learn, i am getting this ModuleNotFoundError: No module named 'scipy'
Checked the path where the devshell python3 is looking (poky/build/tmp-glibc/work/aarch64-oe-linux/python3-scikit-learn/0.23.2-r0/recipe-sysroot-native/usr/lib/python3.8/site-packages), and i can only see the numpy package there, but scipy package is not there.
ls command output :
numpy
numpy-1.17.4-py3.8.egg-info
pkg_resources
__pycache__
README.txt
setuptools
setuptools-45.2.0-py3.8.egg-info
Can someone point me on how to include the python3-scipy package, so that it will be included/copied to the devshell. Or do I need to update/fix something else.
Appreciate any guidance on this.
you can also run:
bitbake -c devshell python3-scipy
and see exactly where the recipe is packaging everything into the rootfs. The rootfs is by default this:
https://git.yoctoproject.org/cgit/cgit.cgi/poky/tree/meta/conf/bitbake.conf#n457
IMAGE_ROOTFS = "${WORKDIR}/rootfs"
so check out what python3-scipy puts into ${WORKDIR}/rootfs (${WORKDIR} is where you get thrown into after you execute devshell, so just cd into rootfs from there).
If python3-scipy puts it into somewhere that is not on the PATH, you can add that to your path.
you can see how python3-scipy looks for libraries:
https://github.com/gpanders/meta-scipy/blob/1c07824202af668ef1539c3de392cf737c5ba3fd/recipes-devtools/python/python3-scipy_1.5.3.bb#L29
# Tell Numpy to look in target sysroot site-packages directory for libraries
LDFLAGS_append = " -L${STAGING_LIBDIR}/${PYTHON_DIR}/site-packages/numpy/core/lib"
Related
Here's my setup.py
setup(
name='shipane_sdk',
version='1.0.0.a5',
# ...
data_files=[(os.path.join(os.path.expanduser('~'), '.shipane_sdk', 'config'), ['config/scheduler-example.ini'])],
# ...
)
Packing & Uploading commands:
python setup.py sdist
python setup.py bdist_wheel --universal
twine upload dist/*
Installing command:
pip install shipane_sdk
But, it doesn't install the config/scheduler-example.ini under ~/.shipane_sdk
The pip documents says:
setuptools allows absolute “data_files” paths, and pip honors them as
absolute, when installing from sdist. This is not true when installing
from wheel distributions. Wheels don’t support absolute paths, and
they end up being installed relative to “site-packages”. For
discussion see wheel Issue #92.
Do you know how to do installing from sdist?
There are multiple solutions to this problem and it is all very confusing how inconsistent the packaging tools work. Some time ago I found the following workaround worked for me best with sdist (note that it doesn't work with wheels!):
Instead of using data_files, attach the files to your package using MANIFEST.in, which in your case could look like this:
include config/scheduler-example.ini
Copy the files "manually" to chosen location using this snippet in setup.py:
if 'install' in sys.argv:
from pkg_resources import Requirement, resource_filename
import os
import shutil
# retrieve the temporary path where the package has been extracted to for installation
conf_path_temp = resource_filename(Requirement.parse(APP_NAME), "conf")
# if the config directory tree doesn't exist, create it
if not os.path.exists(CONFIG_PATH):
os.makedirs(CONFIG_PATH)
# copy every file from given location to the specified ``CONFIG_PATH``
for file_name in os.listdir(conf_path_temp):
file_path_full = os.path.join(conf_path_temp, file_name)
if os.path.isfile(file_path_full):
shutil.copy(file_path_full, CONFIG_PATH)
In my case "conf" was the subdirectory in the package that contained my data files and they were supposed to be installed into CONFIG_PATH which was something like /etc/APP_NAME
I'm trying to run a script that requires the datasets python package. I've tried installing this unsuccessfully using pip by calling:
pip install datasets
I know this hasn't worked because when I run the script I get the message:
Traceback (most recent call last):
File "lda.py", line 2, in <module>
import lda
File "/Users/deepthought/lda.py", line 3, in <module>
import datasets
ImportError: No module named datasets
I've installed python via homebrew.
When I run pip install datasets I get the error:
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/ch/84cpkwc52zx0rsh4k5v4_7h40000gn/T/pip-build-gZWyT3/datasets/
I'm fairly new to scripting python or going under the hood of an OS X, so there's a risk I've missed something elementary.
I've been researching & trying to overcome this for about a week now including looking at similar questions on stackoverflow.com and haven't gotten past this stage for the duration. One of the tutorials I was working through told me to edit ~/.profile
This has been left like so:
# The orginal version is saved in .profile.pysave
#PATH="/Library/Frameworks/Python.framework/Versions/3.5/bin:${PATH}"
#export PATH
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
/etc/paths contains:
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
I'm running OS X El Capitan - 10.11.5 (15F34)
Python 2.7.11
Brew doctor flagged multiple items, but I've no idea whether it is worth fixing none/all of them:
Warning: Your XQuartz (2.7.7) is outdated
Please install XQuartz 2.7.9:
https://xquartz.macosforge.org
Warning: Python is installed at /Library/Frameworks/Python.framework
Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libtcl8.6.dylib
/usr/local/lib/libtk8.6.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/fakemysql.h
/usr/local/include/fakepq.h
/usr/local/include/fakesql.h
/usr/local/include/itcl.h
/usr/local/include/itcl2TclOO.h
/usr/local/include/itclDecls.h
/usr/local/include/itclInt.h
/usr/local/include/itclIntDecls.h
/usr/local/include/itclMigrate2TclCore.h
/usr/local/include/itclTclIntStubsFcn.h
/usr/local/include/mysqlStubs.h
/usr/local/include/node/ares.h
/usr/local/include/node/ares_version.h
/usr/local/include/node/nameser.h
/usr/local/include/node/node.h
/usr/local/include/node/node_buffer.h
/usr/local/include/node/node_internals.h
/usr/local/include/node/node_object_wrap.h
/usr/local/include/node/node_version.h
/usr/local/include/node/openssl/opensslconf.h
/usr/local/include/node/uv-private/ngx-queue.h
/usr/local/include/node/uv-private/stdint-msvc2008.h
/usr/local/include/node/uv-private/tree.h
/usr/local/include/node/uv-private/uv-bsd.h
/usr/local/include/node/uv-private/uv-darwin.h
/usr/local/include/node/uv-private/uv-linux.h
/usr/local/include/node/uv-private/uv-sunos.h
/usr/local/include/node/uv-private/uv-unix.h
/usr/local/include/node/uv-private/uv-win.h
/usr/local/include/node/uv.h
/usr/local/include/node/v8-debug.h
/usr/local/include/node/v8-preparser.h
/usr/local/include/node/v8-profiler.h
/usr/local/include/node/v8-testing.h
/usr/local/include/node/v8.h
/usr/local/include/node/v8stdint.h
/usr/local/include/node/zconf.h
/usr/local/include/node/zlib.h
/usr/local/include/odbcStubs.h
/usr/local/include/pqStubs.h
/usr/local/include/tcl.h
/usr/local/include/tclDecls.h
/usr/local/include/tclOO.h
/usr/local/include/tclOODecls.h
/usr/local/include/tclPlatDecls.h
/usr/local/include/tclThread.h
/usr/local/include/tclTomMath.h
/usr/local/include/tclTomMathDecls.h
/usr/local/include/tdbc.h
/usr/local/include/tdbcDecls.h
/usr/local/include/tdbcInt.h
/usr/local/include/tk.h
/usr/local/include/tkDecls.h
/usr/local/include/tkPlatDecls.h
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/tcl.pc
/usr/local/lib/pkgconfig/tk.pc
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
git
python3
Warning: Broken symlinks were found. Remove them with `brew prune`:
/usr/local/bin/github
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/usr/local/lib/perl5/site_perl/Git/IndexInfo.pm
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/usr/local/lib/perl5/site_perl/Git/SVN/Fetcher.pm
/usr/local/lib/perl5/site_perl/Git/SVN/GlobSpec.pm
/usr/local/lib/perl5/site_perl/Git/SVN/Log.pm
/usr/local/lib/perl5/site_perl/Git/SVN/Memoize/YAML.pm
/usr/local/lib/perl5/site_perl/Git/SVN/Migration.pm
/usr/local/lib/perl5/site_perl/Git/SVN/Prompt.pm
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/usr/local/share/git-core/templates/hooks/pre-commit.sample
/usr/local/share/git-core/templates/hooks/pre-push.sample
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/usr/local/share/git-core/templates/hooks/prepare-commit-msg.sample
/usr/local/share/git-core/templates/hooks/update.sample
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Warning: Your Homebrew is outdated.
You haven't updated for at least 24 hours. This is a long time in brewland!
To update Homebrew, run `brew update`.
How do I make progress in diagnosing the issue with the installation of the datasets package?
Update
Here is the script I'm trying to run:
import sys
egg_path = '/usr/local/lib/python2.7/site-packages/datasets-0.0.9-py2.7.egg'
sys.path.append(egg_path)
import numpy as np
import lda
import datasets
X = lda.datasets.load_reuters()
vocab = lda.datasets.load_reuters_vocab()
titles = lda.datasets.load_reuters_titles()
X.shape
(395, 4258)
X.sum()
84010
model = lda.LDA(n_topics=20, n_iter=1500, random_state=1)
model.fit(X) # model.fit_transform(X) is also available
topic_word = model.topic_word_ # model.components_ also works
n_top_words = 8
for i, topic_dist in enumerate(topic_word):
topic_words = np.array(vocab)[np.argsort(topic_dist)][:-(n_top_words+1):-1]
print('Topic {}: {}'.format(i, ' '.join(topic_words)))
Using pip install datasets I was also not able to properly install this package. It seems like there is a bug in this particular package.
The DESCRIBE.rst file is simply missing. To fix this just download the plain package from PyPi. https://pypi.python.org/pypi/datasets/0.0.9
Then adjust the setup.py file (remove the description).
Afterwards you need to install using python setup.py install. Don't forget to add the installed package to your Python path!
To do so, I would recommend that you add the following to your script.
import sys
egg_path = '__MODULE_PATH__/datasets-0.0.9-py3.5.egg'
sys.path.append(egg_path)
import datasets
Otherwise, you can also add your module using:
export PATH=__MODULE_PATH__:$PATH
Alternatively, you could also simply pull the source code from the Github repository and just include it in your project. https://github.com/realtimeweb/datasets
Hope this was kind of helpful to your problem. If you got any further questions just let me know.
I just hit the same issue on a rapsberry pi, just found out this had been fixed but the error comes from the lack of ram to extract properly the package.
You can fix this by disabling the creation of a cache dir in ram adding the parameter
--no-cache-dir
for example
pip2 install --user --no-cache-dir datasets
I am trying to install pdfMiner to work with CollectiveAccess. My host (pair.com) has given me the following information to help in this quest:
When compiling, it will likely be necessary to instruct the
installation to use your account space above, and not try to install
into the operating system directories. Typically, using "--
home=/usr/home/username/pdfminer" at the end of the install command
should allow for that.
I followed this instruction when trying to install.
The result was:
running install
running build
running build_py
running build_scripts
running install_lib
running install_scripts
changing mode of /usr/home/username/pdfminer/bin/latin2ascii.py to 755
changing mode of /usr/home/username/pdfminer/bin/pdf2txt.py to 755
changing mode of /usr/home/username/pdfminer/bin/dumppdf.py to 755
running install_egg_info
Removing /usr/home/username/pdfminer/lib/python/pdfminer-20140328.egg-info
Writing /usr/home/username/pdfminer/lib/python/pdfminer-20140328.egg-info
I don't see anything wrong with that (I'm very new to python), but when I try to run the sample command $ pdf2txt.py samples/simple1.pdf I get this error:
Traceback (most recent call last): File "pdf2txt.py", line 3, in <module>
from pdfminer.pdfdocument import PDFDocument ImportError: No module named pdfminer.pdfdocument
I'm running python 2.7.3. I can't install from root (shared hosting). The most recent version of pdfminer, which is 2014/03/28.
I've seen some posts on similar issues ("no module named. . . " but nothing exactly the same. The proposed solutions either don't help (such as installing with sudo - not an option; specifying the path for python (which doesn't seem to be the issue), etc.).
Or is this a question for my host? (i.e., something amiss or different about their setup)
I had an error like this:
No module named 'pdfminer.pdfinterp'; 'pdfminer' is not a package
My problem was that I had named my script pdfminer.py which for the reasons that I don't know, Python took it for the original pdfminer package files and tried to compiled it.
I renamed my script to something else, deleted all the *.pyc file and __pycache__ directory and my problem was solved.
use this command worked for me and removed the error
pip install pdfminer.six
Since the package pdfminer is installed to a non-standard/non-default location, Python won't be be able to find it. In order to use it, you will need to add it to your 'pythonpath'. Three ways:
At run time, put this in your script pdf2txt.py:
import sys
# if there are no conflicting packages in the default Python Libs =>
sys.path.append("/usr/home/username/pdfminer")
or
import sys
# to always use your package lib before the system's =>
sys.path.insert(1, "/usr/home/username/pdfminer")
Note: The install path specified with --home is used as the Lib for all packages which you might want to install, not just this one. You should delete that folder and re-install with --
home=/usr/home/username/myPyLibs (or any generic name) so that when you install other packages with that install path, you would only need the one path to add to your local Lib to be able to import them:
import sys
sys.path.insert(1, "/usr/home/username/myPyLibs")
Add it to PYTHONPATH before executing your script:
export PYTHONPATH="${PYTHONPATH}:/usr/home/username/myPyLibs"
And then put that in your ~/.bashrc file (/usr/home/username/.bashrc) or .profile as applicable. This may not work for programs which are not executed from the console.
Create a VirtualEnv and install the packages you need to that.
I have a virtual environment and I had to activate it before I did a pip3 install to have the venv see it.
source ~/venv/bin/activate
We have a setup.py file for one of our Python modules. In setup.py we are actually using the numpy module to do some setup. The module itself also utilizes numpy.
The setup.py works fine on our host machines.
However, when we run the following bitbake recipe for our embedded platform, the build fails as it cannot find numpy. I checked and I cannot find what the PYTHONPATH variable is set to. Running bitbake -e | grep ^PYTHONPATH= returns nothing; so perhaps this is the problem?
It may be that we are going about this wrong as well. Any insight into why its not working or advice on how to accomplish using bitbake with our setup.py would be greatly appreciated.
Our recipe. I tried to use the matplotlib recipe as a baseline as I know that matplotlib has a numpy dependency.
DESCRIPTION = "our-pythonlib"
AUTHOR = "Author"
MAINTAINER = "${AUTHOR}"
SECTION = "company-apps"
LICENSE = "CLOSED"
S="${THISDIR}/our-pythonlib"
inherit distutils
# depend on following packages to work:
RDEPENDS_${PN} += " \
python-numpy \
python-ctypes \
python-json \
"
EXTRA_OECONF = "--disable-docs --with-python-includes=${STAGING_INCDIR}/../"
inherit distutils
do_compile_prepend() {
BUILD_SYS=${BUILD_SYS} HOST_SYS=${HOST_SYS} \
${STAGING_BINDIR_NATIVE}/python setup.py build ${DISTUTILS_BUILD_ARGS} || \
true
}
# need to export these variables for python-config to work
export PYTHONPATH
export BUILD_SYS
export HOST_SYS
export STAGING_INCDIR
I am bitbaking a couple of python libraries and got this warning while adding second one of them:
WARNING: The recipe is trying to install files into a shared area when those files already exist. Those files are:
/home/ilya/beaglebone-dany/build/tmp/sysroots/beaglebone/usr/lib/python2.7/site-packages/site.py
/home/ilya/beaglebone-dany/build/tmp/sysroots/beaglebone/usr/lib/python2.7/site-packages/site.pyo
The libraries both use inherit distutils. So this is okay as far as bitbake goes, but when I tried to install the second package via opkg, I got this error:
# opkg install http://yocto.local:8080/python-requests_1.2.0-r0_armv7a-vfp-neon.ipk
Downloading http://yocto.local:8080/python-requests_1.2.0-r0_armv7a-vfp-neon.ipk.
Installing python-requests (1.2.0-r0) to root...
Configuring python-requests.
# opkg install http://yocto.local:8000/python-mylib_0.0.1-r0_armv7a-vfp-neon.ipk
Downloading http://yocto.local:8080/python-mylib_0.0.1-r0_armv7a-vfp-neon.ipk.
Installing python-mylib (0.0.1-r0) to root...
Collected errors:
* check_data_file_clashes: Package mylib-python wants to install file /usr/lib/python2.7/site-packages/site.py
But that file is already provided by package * python-requests
* check_data_file_clashes: Package mylib-python wants to install file /usr/lib/python2.7/site-packages/site.pyo
But that file is already provided by package * python-requests
* opkg_install_cmd: Cannot install package mylib-python.
Both recipes look just like so:
DESCRIPTION = "Requests: HTTP for Humans"
HOMEPAGE = "http://docs.python-requests.org/en/latest/"
SECTION = "devel/python"
LICENSE = "Apache-2.0"
DEPENDS = "python"
RDEPENDS_${PN} = "python-core"
PR = "r0"
SRC_URI = "git://github.com/kennethreitz/requests;protocol=git"
S = "${WORKDIR}/git/"
inherit distutils
#NOTE: I'm not 100% sure whether I still need to export these?
export BUILD_SYS
export HOST_SYS
export STAGING_INCDIR
export STAGING_LIBDIR
BBCLASSEXTEND = "native"
I have copied this from pycurl recipe, which also have had these lines that I removed:
do_install_append() {
rm -rf ${D}${datadir}/share
}
To get rid of the conflicting /usr/lib/python2.7/site-packages/site.py, one needs to avoid shipping this file by doing this:
do_install_append() {
rm -f ${D}${libdir}/python*/site-packages/site.py*
}
There had been another issue with the original version of recipe, the files it installed contained just .egg directory. I wasn't able to import the resulting package.
It turns out that using inherit setuptools instead of inherit distutils works.
I'm not a Python expert, but all setuptools class does is just this:
inherit distutils
DEPENDS += "python-setuptools-native"
DISTUTILS_INSTALL_ARGS = "--root=${D} \
--single-version-externally-managed \
--prefix=${prefix} \
--install-lib=${PYTHON_SITEPACKAGES_DIR} \
--install-data=${datadir}"
It turns out that some modules (e.g. PyBBIO) do not recognise --single-version-externally-managed, so then you have to use inherit distutils and you do get a working package.
Below is full recipe for the python-requests package which should soon be available upstream, in case you are intending to use it.
DESCRIPTION = "Requests: HTTP for Humans"
HOMEPAGE = "http://docs.python-requests.org/en/latest/"
SECTION = "devel/python"
LICENSE = "Apache-2.0"
#DEPENDS = "python-core"
RDEPENDS_${PN} = "python"
PR = "r0"
SRC_URI = "git://github.com/kennethreitz/requests;protocol=git"
S = "${WORKDIR}/git/"
inherit setuptools
# need to export these variables for python-config to work
export BUILD_SYS
export HOST_SYS
export STAGING_INCDIR
export STAGING_LIBDIR
BBCLASSEXTEND = "native"
do_install_append() {
rm -f ${D}${libdir}/python*/site-packages/site.py*
}