Installing PyGMO on Mac OS X Yosemite - missing boost-python3?

Installing PyGMO on Mac OS X Yosemite - missing boost-python3? - python

I've been trying to install PyGMO on my Mac OS X 10.10. I'm using Anaconda Python 2.3, so it comes with python 3.4.
I followed the instructions on http://esa.github.io/pygmo/install.html and did try to build boost manually but didn't have much luck with building boost-python... The instructions I could find on the official website was very limited...
While using ccmake to run the build file in pagmo/build directory, it complained that it did not find boost-python3...
So I reverted to using brew to install boost. Thanks to the info I found on this page: http://ryanclouser.com/2015/07/16/Mac-OSX-Build-Boost-Python-with-Python3-Support/
Now I have both boost and boost-python installed, but still the ccmake process for PyGMO complains about not being able to find boost-python3.
Are there any environment variables I need to set? In the ccmake config screen do I need to set Boost_PYTHON3_LIBRARY_RELEASE or Boost_PYTHON3_LIBRARY_DEBUG?
LATEST EDIT: This SHA256 below mis-match is resolved. Turned out it was caused by source forge site being down when I ran the commands... Some better error messages would have helped.
However, when I tried to get boost and boost-python with brew, I got the following SHA256 hash code mismatch error.
Anyone has any idea how to fix this?
>$ sudo brew install boost-python --with-python3
==> Installing boost-python dependency: boost
==> Downloading https://homebrew.bintray.com/b...
####################################################################### 100.0%
==> Pouring boost-1.58.0.yosemite.bottle.tar.gz
🍺 /usr/local/Cellar/boost/1.58.0: 10718 files, 486M
==> Installing boost-python
==> Downloading https://downloads.sourceforge....
==> Downloading from http://downloads.sourceforge.n...
####################################################################### 100.0%
Error: SHA256 mismatch
Expected: fdfc204fc33ec79c99b9a74944c3e54bd78be4f7f15e260c0e2700a36dc7d3e5
Actual: 818a4b8bbcb50878a8b1b9f71b4274d242ab46bf860c74676e98dec1d0248821
Archive: /Library/Caches/Homebrew/boost-python-1.58.0.tar.bz2
To retry an incomplete download, remove the file above.
Tried to delete the cached boost package files as suggested a few times but it didn't work either.
Thanks guys.

Ok problem resolved. Here's the best practice to get boost on Mac OS X.
Use Homebrew! but the key is to use the --with-python3 switch! Credits to this page: http://ryanclouser.com/2015/07/16/Mac-OSX-Build-Boost-Python-with-Python3-Support/
>$ brew install boost-python --with-python3
Assuming you have CMake already, just follow the instructions on PyGMO's website.
pagmo/build>$ ccmake ../
This will then bring up the config screen, everything should look fine. If not, do rm -rf * in pagmo/build folder to clear everything and start again (this resolved the issue with boost-python3 for me mentioned above.
Then run make and sudo make install as mentioned on the website.
PyGMO should be ready for use in python after that!
I had the following error message. However, if I start python in the ~/anaconda/lib folder where I have my anaconda installed, import PyGMO worked, so it's probably some library path thing that needs to be fixed.
>>> import PyGMO as gmo
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/xxx/anaconda/lib/python3.4/site-packages/PyGMO/__init__.py", line 57, in <module>
from PyGMO import core, algorithm, migration, problem, topology, test, util
File "/Users/xxx/anaconda/lib/python3.4/site-packages/PyGMO/core/__init__.py", line 2, in <module>
from PyGMO.core._core import *
ImportError: dlopen(/Users/xxx/anaconda/lib/python3.4/site-packages/PyGMO/core/_core.so, 2):
Library not loaded: libpython3.4m.dylib
Referenced from: /Users/xxx/anaconda/lib/python3.4/site-packages/PyGMO/core/_core.so
Reason: image not found
**Latested EDIT: ** Did some searching around, a partial solution to the import error above, is to set DYLD_LIBRARY_PATH=~/anaconda/lib. With this, imports will work when you launch python in a console. However, IPython-notebook would not start for me... Also have seen that Max OS doesn't really have a dynamic search also...

Related

Cannot install custom python module

I am having trouble installing a custom python module I have written.
Here are my steps so far:
Navigate to the module directory C:\Users\myname\repos\mymodulename where the setup.py file is in the anaconda prompt. Type: python setup.py install
The command prompt returns (plus some other things)
Extracting mymodulename-0.1-py3.7.egg to c:\users\myname\appdata\local\continuum\anaconda3\lib\site-packages
mymodulename 0.1 is already the active version in easy-install.pth
Installing myclass-script.py script to C:\Users\myname\AppData\Local\Continuum\anaconda3\Scripts
Installing myclass.exe script to C:\Users\myname\AppData\Local\Continuum\anaconda3\Scripts
Installed c:\users\myname\appdata\local\continuum\anaconda3\lib\site-packages\mymodulename-0.1-py3.7.egg
Processing dependencies for mymodulename==0.1
...
Using c:\users\myname\appdata\local\continuum\anaconda3\lib\site-packages
Finished processing dependencies for mymodulename==0.1
To me that looks like it has installed. Opening up the console and trying to import:
>>> import mymodulename.myclassas ce
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'mymodulename'
>>>
It appears in hasn't. Checking the list of modules in anaconda with help('modules') confirms that it has not been imported.
I thought that perhaps i had installed it to the wrong environment:
(base) C:\Users\myname>conda env list
# conda environments:
#
base * C:\Users\myname\AppData\Local\Continuum\anaconda3
py2 C:\Users\myname\AppData\Local\Continuum\anaconda3\envs\py2
Only a python 2 environment which mymodule wouldn't be compatible with.
Does anyone have any suggestions about what I can try to resolve this? Happy to elaborate on any of the points
Thanks in advance.
EDIT: Some more information that may be relevant.
This package was initially installed in site-packages. I have reinstalled there and the package works. The reason I moved the package is because I am aware it is bad practice to store custom packages there.

Problems with Python: ImportError: No module named ... [Linux]

I am a noob with installing python programs. I know there are a lot of Questions like this here, I have tried to find a solution for my problem but I can't fix it.
First of all, I am trying to install a program called Qarq. The readme says:
Setup
In order to get qark running, it must be present on your python path. If not, it may lead to module not found errors. This can be done for your current shell by running the following:
export PYTHONPATH={qark root directory}:$PYTHONPATH
Well, I type the command. I check the variable with an echo and I can see the directory in the variable. However, I type "python setup.py install" and I get this error:
santoku#santoku-PC:~/qark$ python setup.py install
Traceback (most recent call last):
File "setup.py", line 1, in <module>
from setuptools import setup, find_packages
ImportError: No module named setuptools
Then, I read in a question here that you must install setuptools, so I did it. I ran the next command:
sudo apt-get install python-setuptools
But the problem is still there, I try to run "python setup.py install" and I get the same error.
On the other hand, the readme says you only need to execute "$ python qarkMain.py". I do that and I get the same error with different module:
santoku#santoku-PC:~/qark/qark$ python qarkMain.py install
Traceback (most recent call last):
File "qarkMain.py", line 30, in <module>
from qark.modules.IssueType import IssueSeverity
ImportError: No module named qark.modules.IssueType
I am using Python 2.7.12 (default, Nov 12 2016, 01:02:22) [GCC 4.8.4] on linux2. (Ubuntu 14.04.5 LTS)
I have tried to install qark on Ubuntu 16.04.1 LTS and it worked perfectly. I didn't need to install setuptools. Both have the same python version.
I guess the problem is python can't find the modules, maybe I have to move the qark directory to another directory.
I think that's all, if you need more extra information just ask me.
I need your help, I am sure my problem is a foolishness and easy to fix. But I am a noob with python and I don't have any idea.
Thank you very much and thanks in advance.
Sorry for my English, I am not a native speaker.
EDIT: I found a solution, I tried to install again the OS and now python works properly, I don't know if I broke python or I did something bad. Anyway, Thanks.

i could get it work typing this:
1) PYTHONPATH=\home\santoku\qark\qark\:$PYTHONPATH
then just type:
2) python qarkMain.py

Install SCIP solver on Python3.5 Numberjack (OSX)

I am learning Constraint Programming in Python and, for the solving of the problems, I am supposed to use the SCIP solver. I have installed the Numberjack standard package from Github witch includes Mistral, Mistral2, Toulbar2, MipWrapper, SatWrapper, MiniSat and Walksat solvers.
Running my code I got the following error:
Traceback (most recent call last):
File "/Users/angelocoelho/anaconda3/lib/python3.5/site-packages/Numberjack/__init__.py", line 910, in load
lib = __import__(solverstring, fromlist=[solverspkg])
ImportError: No module named 'Numberjack.solvers.SCIP'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "grafosdefluxos.py", line 42, in <module>
solver = model.load('SCIP')
File "/Users/angelocoelho/anaconda3/lib/python3.5/site-packages/Numberjack/__init__.py", line 915, in load
solvername)
ImportError: ERROR: Failed during import, wrong module name? (SCIP)
I already ran make in 'scipoptsuite-3.1.0' and in 'scip-3.2.1', installed Numberjack-master's 'setup.py' and tried this:
python setup.py -solver SCIP
witch returned the error
Error: the solver 'SCIP' is not known, please use one of: Mistral, SatWrapper, Toulbar2, Walksat, MipWrapper, MiniSat, Mistral2
I have the SCIP folders alongside and inside the Numberjack folders.
I read and ran all the commands in the README and INSTALL files on how I could get this solver configured but I couldn't get it right.
How can I get SCIP available to solve the problems in Numberjack?

After talking to the assistant teacher I got the answer for this problem.
The folder where Numberjack/SCIP was being installed was not the one it was supposed to be, therefore it was not really included in the solver list. After completing the python setup.py build and python setup.py install installation I ran python setup.py build -solver SCIP and the terminal feedback stated
Successfully built solver interfaces for MipWrapper, SCIP
But the jupyter notebook didn't recognize the solver.
What solution should work having Anaconda (python3.5) already installed:
Download Numberjack (file "Numberjack-master.zip") and unpack it.
Download SCIP and copy the downloaded file, scipoptsuite-3.1.0.tgz. Paste it inside Numberjack-master unpacked directory. The path of it should be ~/Downloads/Numberjack-master/scipoptsuite-3.1.0.tgz.
In terminal run cd ~/Downloads/Numberjack-master (or your Numberjack-master directory path).
Then run python3.5 setup.py install --user.
In my case Jupyter was looking for the solvers in
~/anaconda3/lib/python3.5/site-packages/Numberjack/ and they were
not being installed there so, instead of using python, I used python3.5 since my Anaconda was the Python 3.5 package.

Why is there a scip-3.2.1 directory? The SCIP Opt Suite 3.1.0 contains SCIP 3.1.0. You need to make sure to run all setup and make commands exactly as stated on the Numberjack install page.

Can't install datasets package via pip

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/
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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
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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
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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
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/usr/local/share/man/man1/git-remote.1
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/usr/local/share/man/man1/git-repo-config.1
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/usr/local/share/man/man1/git-rev-list.1
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/usr/local/share/man/man1/git-revert.1
/usr/local/share/man/man1/git-rm.1
/usr/local/share/man/man1/git-send-email.1
/usr/local/share/man/man1/git-send-pack.1
/usr/local/share/man/man1/git-sh-i18n--envsubst.1
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/usr/local/share/man/man1/gitweb.1
/usr/local/share/man/man3/Git.3pm
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/usr/local/share/man/man3/Git::SVN::Editor.3pm
/usr/local/share/man/man3/Git::SVN::Fetcher.3pm
/usr/local/share/man/man3/Git::SVN::Memoize::YAML.3pm
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/usr/local/share/man/man3/Git::SVN::Utils.3pm
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/usr/local/share/man/man7/gitcredentials.7
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/usr/local/share/man/man7/gitdiffcore.7
/usr/local/share/man/man7/gitglossary.7
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/usr/local/share/man/man7/gitworkflows.7
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

Unable to import git in python

I am facing these issues. Can you help me with the same ?
Why am I seeing this error ? Do I have to add anything in the requirements.txt file ?
>>> import git
Traceback (most recent call last):
File "<pyshell#7>", line 1, in <module>
import git
File "git\__init__.py", line 29, in <module>
_init_externals()
File "git\__init__.py", line 23, in _init_externals
raise ImportError("'gitdb' could not be found in your PYTHONPATH")
ImportError: 'gitdb' could not be found in your PYTHONPATH
>>> from git import Repo
Traceback (most recent call last):
File "<pyshell#8>", line 1, in <module>
from git import Repo
File "git\__init__.py", line 29, in <module>
_init_externals()
File "git\__init__.py", line 23, in _init_externals
raise ImportError("'gitdb' could not be found in your PYTHONPATH")
ImportError: 'gitdb' could not be found in your PYTHONPATH

I already had gitdb and smmap installed so I had to reinstall them.
You can reinstall them by running the following command in your terminal:
pip3 install --upgrade --force-reinstall gitdb; pip3 install --upgrade --force-reinstall smmap

I also got the message ImportError: 'gitdb' could not be found in your PYTHONPATH (when trying to use GitPython).BUT I had gitdb already installed!
Thanks to this hint I figured out that gitdb silently failed because it was missing smmap.
So I installed this and it worked.

You need to install gitdb package.
$ sudo easy_install gitdb

I had the same problem. However, gitdb and smmap were already installed by pip. As I used brew to install python and its dependencies on my mac, when I checked brew doctor command, it said that my /usr/local/sbin directory is not in my PATH. So I added it to my PATH (though it didn't have anything to do with the python) and everything worked out eventually.

MS Windows Versions of this problem can occur because of the order of Python versions in your system PATH, as it did for me. I did not realize that when I installed another program, it installed a newer version of Python for its own usage, and it appended my system PATH with the address to the newer version. I noticed it when I looked at the PATH variable and found two versions of Python being called. Windows uses the first it finds, and if the first doesn't match what your program expects, it gets confused and can't find the right path to the module. This is what I did to resolve it:
To check: an easy way to test if this is your problem is to see if the paths separated by semicolons are in the right order. That can be seen in the System Variables of Windows or by printing your PATH variable in your CMD shell like in this example:
C:> path
PATH=C:\Program Files (x86)\Python37-32\Scripts;C:\Program Files (x86)\Python37-32;C:\Program Files\Python38\Scripts;C:\WINDOWS
Temporary solution:
To see if it is going to fix your computer, change it in your CMD window. Your variable change will be discarded when the window is closed. One way to do this test is to copy the paths, move the Python references to the order they are needed, and write it back:
C:> set path = C:\WINDOWS;C:\Program Files (x86)\Python37-32;C:\Program Files\Python38\Scripts;C:\Program Files (x86)\Python37-32\Scripts\
Then run the Python program to see if this was your problem. Note that this is only an example; do not copy & paste it. Your path is customized for the programs on your computer.
Permanent solution: If the above test resolves your problem, you must change your System Variables to make the change permanent. For me that usually requires a reboot afterwards in order to make the variables appear in all new windows.

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