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So I'm trying to install FEniCS from the instructions here. I did the
pip3 install fenics-ffc --upgrade
inside my virtualenv and it worked but when I try to import dolfin I get a ModuleNotFound error. I'm not sure how to get dolfin installed. I did
pip install pybind11
to get pybind11 installed then copied the code for dolfin installation into my cmd
FENICS_VERSION=$(python3 -c"import ffc; print(ffc.__version__)")
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/dolfin
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/mshr
mkdir dolfin/build && cd dolfin/build && cmake .. && make install && cd ../..
mkdir mshr/build && cd mshr/build && cmake .. && make install && cd ../..
cd dolfin/python && pip3 install . && cd ../..
cd mshr/python && pip3 install . && cd ../..
but it just spat out dozens of errors like:
FENICS_VERSION=$(python3 -c"import ffc; print(ffc.version)") 'FENICS_VERSION' is not recognized as an internal or external command, operable program or batch file.
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/dolfin Cloning into 'dolfin'...
fatal: Remote branch $FENICS_VERSION not found in upstream origin
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/mshr Cloning into 'mshr'...
fatal: Remote branch $FENICS_VERSION not found in upstream origin
There were lots more errors after too. Am I not supposed to paste the dolfin code into cmd? I don't know much about this stuff so unsure of how to get the dolfin module. I've previously only used pip to get my packages but this does not work for dolfin as it doesn't appear to be on PyPI.
Do you have cmake? It says in the docs you need it. Also its says to to this to install pybind11 not pip install pybind11
For building optional Python interface of DOLFIN and mshr, pybind11 is needed since version 2018.1.0. To install it:
wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz
tar -xf v${PYBIND11_VERSION}.tar.gz && cd pybind11-${PYBIND11_VERSION}
mkdir build && cd build && cmake -DPYBIND11_TEST=off .. && make install
Also what is your os?
So here is how you can install fenics 2019.1 using conda (miniconda):
Install Conda:
First go to https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
and follow the installation instructions.
Create a conda environment for fenics:
Open a terminal and type:
conda create -n fenics
To activate the created environment "fenics", type:
conda activate fenics
If you want the fenics environment to be activated automatically everytime you open a new terminal, then open you .bashrc file (should be under /home/username/.bashrc) and add the line "source activate fenics" below the ">>> conda initialize >>>" block.
Install fenics:
Type all these commands:
conda install -c conda-forge h5py=*=*mpich*
conda install -c conda-forge fenics
pip install meshio
pip install matplotlib
pip install --upgrade gmsh
conda install -c conda-forge paraview
pip install scipy
The second command will take a while. I added a few nice to have programs like gmsh and paraview which will help you to create meshes and view your solutions.
How do I uninstall all packages installed by pip from my currently activated virtual environment?
I've found this snippet as an alternative solution. It's a more graceful removal of libraries than remaking the virtualenv:
pip freeze | xargs pip uninstall -y
In case you have packages installed via VCS, you need to exclude those lines and remove the packages manually (elevated from the comments below):
pip freeze | grep -v "^-e" | xargs pip uninstall -y
If you have packages installed directly from github/gitlab, those will have #.
Like:
django # git+https://github.com/django.git#<sha>
You can add cut -d "#" -f1 to get just the package name that is required to uninstall it.
pip freeze | cut -d "#" -f1 | xargs pip uninstall -y
This will work for all Mac, Windows, and Linux systems.
To get the list of all pip packages in the requirements.txt file (Note: This will overwrite requirements.txt if exist else will create the new one, also if you don't want to replace old requirements.txt then give different file name in the all following command in place requirements.txt).
pip freeze > requirements.txt
Now to remove one by one
pip uninstall -r requirements.txt
If we want to remove all at once then
pip uninstall -r requirements.txt -y
If you're working on an existing project that has a requirements.txt file and your environment has diverged, simply replace requirements.txt from the above examples with toberemoved.txt. Then, once you have gone through the steps above, you can use the requirements.txt to update your now clean environment.
And For single command without creating any file (As #joeb suggested).
pip uninstall -y -r <(pip freeze)
I wanted to elevate this answer out of a comment section because it's one of the most elegant solutions in the thread. Full credit for this answer goes to #joeb.
pip uninstall -y -r <(pip freeze)
This worked great for me for the use case of clearing my user packages folder outside the context of a virtualenv which many of the above answers don't handle.
Edit: Anyone know how to make this command work in a Makefile?
Bonus: A bash alias
I add this to my bash profile for convenience:
alias pipuninstallall="pip uninstall -y -r <(pip freeze)"
Then run:
pipuninstallall
Alternative for Pipenv
If you are using pipenv, you can run:
pipenv uninstall --all
Alternative for Poetry
If you are using Poetry, run:
poetry env remove --python3.9
(Note that you need to change the version number there to match whatever your Python version is.)
This works with the latest. I think it's the shortest and most declarative way to do it.
virtualenv --clear MYENV
But why not just delete and recreate the virtualenv?
Immutability rules. Besides it's hard to remember all those piping and grepping the other solutions use.
Other answers that use pip list or pip freeze must include --local else it will also uninstall packages that are found in the common namespaces.
So here are the snippet I regularly use
pip freeze --local | xargs pip uninstall -y
Ref: pip freeze --help
I managed it by doing the following:
Create the requirements file called reqs.txt with currently installed packages list
pip freeze > reqs.txt
Then uninstall all the packages from reqs.txt
# -y means remove the package without prompting for confirmation
pip uninstall -y -r reqs.txt
I like this method as you always have a pip requirements file to fall back on should you make a mistake. It's also repeatable, and it's cross-platform (Windows, Linux, MacOs).
Method 1 (with pip freeze)
pip freeze | xargs pip uninstall -y
Method 2 (with pip list)
pip list | awk '{print $1}' | xargs pip uninstall -y
Method 3 (with virtualenv)
virtualenv --clear MYENV
On Windows if your path is configured correctly, you can use:
pip freeze > unins && pip uninstall -y -r unins && del unins
It should be a similar case for Unix-like systems:
pip freeze > unins && pip uninstall -y -r unins && rm unins
Just a warning that this isn't completely solid as you may run into issues such as 'File not found' but it may work in some cases nonetheless
EDIT: For clarity: unins is an arbitrary file which has data written out to it when this command executes: pip freeze > unins
That file that it written in turn is then used to uninstall the aforementioned packages with implied consent/prior approval via pip uninstall -y -r unins
The file is finally deleted upon completion.
I use the --user option to uninstall all the packages installed in the user site.
pip3 freeze --user | xargs pip3 uninstall -y
For Windows users, this is what I use on Windows PowerShell
pip uninstall -y (pip freeze)
First, add all package to requirements.txt
pip freeze > requirements.txt
Then remove all
pip uninstall -y -r requirements.txt
The quickest way is to remake the virtualenv completely. I'm assuming you have a requirements.txt file that matches production, if not:
# On production:
pip freeze > reqs.txt
# On your machine:
rm $VIRTUALENV_DIRECTORY
mkdir $VIRTUALENV_DIRECTORY
pip install -r reqs.txt
Using virtualenvwrapper function:
wipeenv
See wipeenv documentation
Its an old question I know but I did stumble across it so for future reference you can now do this:
pip uninstall [options] <package> ...
pip uninstall [options] -r <requirements file> ...
-r, --requirement file
Uninstall all the packages listed in the given requirements file. This option can be used multiple times.
from the pip documentation version 8.1
(adding this as an answer, because I do not have enough reputation to comment on #blueberryfields 's answer)
#blueberryfields 's answer works well, but fails if there is no package to uninstall (which can be a problem if this "uninstall all" is part of a script or makefile). This can be solved with xargs -r when using GNU's version of xargs:
pip freeze --exclude-editable | xargs -r pip uninstall -y
from man xargs:
-r, --no-run-if-empty
If the standard input does not contain any nonblanks, do not run the command. Normally, the command is run once even if there
is no input. This option is a GNU extension.
pip3 freeze --local | xargs pip3 uninstall -y
The case might be that one has to run this command several times to get an empty pip3 freeze --local.
Best way to remove all packages from the virtual environment.
Windows PowerShell:
pip freeze > unins ; pip uninstall -y -r unins ; del unins
Windows Command Prompt:
pip freeze > unins && pip uninstall -y -r unins && del unins
Linux:
pip3 freeze > unins ; pip3 uninstall -y -r unins ; rm unins
This was the easiest way for me to uninstall all python packages.
from pip import get_installed_distributions
from os import system
for i in get_installed_distributions():
system("pip3 uninstall {} -y -q".format(i.key))
the easy robust way
cross-platform
and work in pipenv as well is:
pip freeze
pip uninstall -r requirement
by pipenv:
pipenv run pip freeze
pipenv run pip uninstall -r requirement
but won't update piplock or pipfile so be aware
Cross-platform support by using only pip:
#!/usr/bin/env python
from sys import stderr
from pip.commands.uninstall import UninstallCommand
from pip import get_installed_distributions
pip_uninstall = UninstallCommand()
options, args = pip_uninstall.parse_args([
package.project_name
for package in
get_installed_distributions()
if not package.location.endswith('dist-packages')
])
options.yes = True # Don't confirm before uninstall
# set `options.require_venv` to True for virtualenv restriction
try:
print pip_uninstall.run(options, args)
except OSError as e:
if e.errno != 13:
raise e
print >> stderr, "You lack permissions to uninstall this package.
Perhaps run with sudo? Exiting."
exit(13)
# Plenty of other exceptions can be thrown, e.g.: `InstallationError`
# handle them if you want to.
On Windows if your path is configured correctly, you can use:
pip freeze > unins && pip uninstall -y -r unins && del unins
This works on my windows system
pip freeze > packages.txt && pip uninstall -y -r packages.txt && del packages.txt
The first part pip freeze > packages.txt creates a text file with list of packages installed using pip along with the version number
The second part pip uninstall -y -r packages.txt deletes all the packages installed without asking for a confirmation prompt.
The third part del packages.txt deletes the just now created packages.txt.
This is the command that works for me:
pip list | awk '{print $1}' | xargs pip uninstall -y
If you're running virtualenv:
virtualenv --clear </path/to/your/virtualenv>
for example, if your virtualenv is /Users/you/.virtualenvs/projectx, then you'd run:
virtualenv --clear /Users/you/.virtualenvs/projectx
if you don't know where your virtual env is located, you can run which python from within an activated virtual env to get the path
In Command Shell of Windows, the command pip freeze | xargs pip uninstall -y won't work. So for those of you using Windows, I've figured out an alternative way to do so.
Copy all the names of the installed packages of pip from the pip freeze command to a .txt file.
Then, go the location of your .txt file and run the command pip uninstall -r *textfile.txt*
If you are using pew, you can use the wipeenv command:
pew wipeenv [env]
I simply wanted to remove packages installed by the project, and not other packages I've installed (things like neovim, mypy and pudb which I use for local dev but are not included in the app requirements). So I did:
cat requirements.txt| sed 's/=.*//g' | xargs pip uninstall -y
which worked well for me.
Select Libraries To Delete From This Folder:
C:\Users\User\AppData\Local\Programs\Python\Python310\Lib\site-packages
Why not just rm -r .venv and start over?
pip uninstall `pip freeze --user`
The --user option prevents system-installed packages from being included in the listing, thereby avoiding /usr/lib and distutils permission errors.
I want to run a setup.py that has several dependency links defined, i.e.:
dependency_links=[
"git+ssh://git#my.gitlab/myproject1.git#v1.4.0#egg=myproject1-1.4.0",
"git+ssh://git#my.gitlab/myproject2.git#v0.2.0#egg=myproject2-0.2.0",
]
My question is whether there is a way to pass this array via command line when running the pip install command as follows (e.g.):
RUN pip install numpy==1.10.1 \
&& pip wheel --find-links="wheelhouse/" --wheel-dir="wheelhouse/" uwsgi \
&& pip wheel --find-links="wheelhouse/" --wheel-dir="wheelhouse/" --process-dependency-links gitlablink1, gitlablink2 .
Facing an HTTPSHandler error while installing python packages using pip, following is the stack trace,
--------desktop:~$ pip install Django==1.3
Traceback (most recent call last):
File "/home/env/.genv/bin/pip", line 9, in <module>
load_entry_point('pip==1.4.1', 'console_scripts', 'pip')()
File "/home/env/.genv/lib/python2.7/site-packages/pkg_resources.py", line 378, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/env/.genv/lib/python2.7/site-packages/pkg_resources.py", line 2566, in load_entry_point
return ep.load()
File "/home/env/.genv/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/home/env/.genv/lib/python2.7/site-packages/pip/__init__.py", line 10, in <module>
from pip.util import get_installed_distributions, get_prog
File "/home/env/.genv/lib/python2.7/site-packages/pip/util.py", line 17, in <module>
from pip.vendor.distlib import version
File "/home/env/.genv/lib/python2.7/site-packages/pip/vendor/distlib/version.py", line 13, in <module>
from .compat import string_types
File "/home/env/.genv/lib/python2.7/site-packages/pip/vendor/distlib/compat.py", line 31, in <module>
from urllib2 import (Request, urlopen, URLError, HTTPError,
ImportError: cannot import name HTTPSHandler
I used to edit Modules/setup.dist file and uncomment SSL code lines and rebuilt it, with reference to following thread : http://forums.opensuse.org/english/get-technical-help-here/applications/488962-opensuse-python-openssl-2.html
OSX + homebrew users:
You can get the latest updates to the recipe:
brew reinstall python
But if you still get the issue, e.g. maybe you have upgraded your OS, then you may need to get the latest openssl first. You can check which version and where it is used from:
openssl version -a
which openssl
To get the latest openssl:
brew update
brew install openssl
brew link --overwrite --dry-run openssl # safety first.
brew link openssl --overwrite
This may issue a warning:
bash-4.3$ brew link --overwrite --dry-run openssl
Warning: Refusing to link: openssl Linking keg-only openssl means you may end up linking against the insecure, deprecated system OpenSSL while using the headers from Homebrew's openssl.
Instead, pass the full include/library paths to your compiler e.g.:
-I/usr/local/opt/openssl/include -L/usr/local/opt/openssl/lib
Side note: this warning means that for other apps, you may want to use
export LDFLAGS=-L/usr/local/opt/openssl/lib
export CPPFLAGS=-I/usr/local/opt/openssl/include
Then recompile python:
brew uninstall python
brew install python --with-brewed-openssl
or for python 3
brew uninstall python3
brew install python3 --with-brewed-openssl
You need to install the OpenSSL header files before building Python if you need SSL support. On Debian and Ubuntu, they are in a package called libssl-dev. You might need some more dependencies, as noted here.
Homebrew
This was probably caused by an upgrade to Mavericks. Here's how I fixed it.
Update OpenSSL
#make a copy of the existing library, just in case
sudo cp /usr/bin/openssl /usr/bin/openssl.apple
# update openssl
brew update
brew install openssl
brew link --force openssl
# reload terminal paths
hash -r
Reinstall Python
Python 3
brew uninstall python3
brew install python3 --with-brewed-openssl
Python 2
brew uninstall python
brew install python --with-brewed-openssl
This answer consolidates all the Stack Exchange answers and comments I found, and is based mostly on this Apple Stack Exchange answer.
I was having this problem on Mac OSX, even after confirming my PATH, etc.
Did a; pip uninstall virtualenv then install virtualenv and it seemed to works now.
At the time I had forced brew to link openssl, unlinked it and virtualenv still seems to work but maybe that's because it was originally linked when I reinstalled it.
You need to install OpenSSl before make and install Python to solve the problem.
On Centos:
yum install openssl openssl-devel -y
source
Another symptom of this problem for me was if I went into the python console of my virtualenv and did import ssl it would error out. Turns out my virtualenv wasn't using the brew version of python, just the default install on my machine. No clue why the default install suddenly stopped working, but here's how I fixed it the problem:
rmvirtualenv myvirtualenv
brew update
brew reinstall python
mkvirtualenv -p /usr/local/Cellar/python/whatever_version_number/bin/python myvirtualenv
It seems your pip requires HTTPSHandler which is part of SSL library.
OSX
On OS X you should link OpenSSL during Python installation (See: #14497).
For Python 2:
brew reinstall python --with-brewed-openssl
pip install --upgrade pip
For Python 3:
brew reinstall python3 --with-brewed-openssl
pip3 install --upgrade pip
You could have multiple Python instances together, to list them run:
brew list | grep ^python
Or list your version via ls -al /usr/local/lib/python*.
I'm using Redhat and have met the same problem.
My solution is :
install openssl and openssl-devel ---- yum install openssl openssl-devel -y
install krb5-devel ---- yum install krb5-devel
change to your python's directory and recompile it ---- make
If I didn't do the 2nd step, when I recompiled my python2.7 , the log would say " fail to build module _ssl".
In many cases this is caused by an out of date virtualenv, here's a script to regenerate your virtualenv(s): https://gist.github.com/WoLpH/fb98f7dc6ba6f05da2b8
Simply copy it to a file (downloadable link above) and execute it like this: zsh -e recreate_virtualenvs.sh <project_name>
#!/bin/zsh -e
if [ ! -d "$PROJECT_HOME" ]; then
echo 'Your $PROJECT_HOME needs to be defined'
echo 'http://virtualenvwrapper.readthedocs.org/en/latest/install.html#location-of-project-directories'
exit 1
fi
if [ "" = "$1" ]; then
echo "Usage: $0 <project_name>"
exit 1
fi
env="$1"
project_dir="$PROJECT_HOME/$1"
env_dir="$HOME/envs/$1"
function command_exists(){
type $1 2>/dev/null | grep -vq ' not found'
}
if command_exists workon; then
echo 'Getting virtualenvwrapper from environment'
# Workon exists, nothing to do :)
elif [ -x ~/bin/mount_workon ]; then
echo 'Using mount workon'
# Optional support for packaged project directories and virtualenvs using
# https://github.com/WoLpH/dotfiles/blob/master/bin/mount_workon
. ~/bin/mount_workon
mount_file "$project_dir"
mount_file "$env_dir"
elif command_exists virtualenvwrapper.sh; then
echo 'Using virtualenvwrapper'
. $(which virtualenvwrapper.sh)
fi
if ! command_exists workon; then
echo 'Virtualenvwrapper not found, please install it'
exit 1
fi
rmvirtualenv $env || true
echo "Recreating $env"
mkvirtualenv $env || true
workon "$env" || true
pip install virtualenv{,wrapper}
cd $project_dir
setvirtualenvproject
if [ -f setup.py ]; then
echo "Installing local package"
pip install -e .
fi
function install_requirements(){
# Installing requirements from given file, if it exists
if [ -f "$1" ]; then
echo "Installing requirements from $1"
pip install -r "$1"
fi
}
install_requirements requirements_test.txt
install_requirements requirements-test.txt
install_requirements requirements.txt
install_requirements test_requirements.txt
install_requirements test-requirements.txt
if [ -d docs ]; then
echo "Found docs, installing sphinx"
pip install sphinx{,-pypi-upload} py
fi
echo "Installing ipython"
pip install ipython
if [ -f tox.ini ]; then
deps=$(python -c "
parser=__import__('ConfigParser').ConfigParser();
parser.read('tox.ini');
print parser.get('testenv', 'deps').strip().replace('{toxinidir}/', '')")
echo "Found deps from tox.ini: $deps"
echo $deps | parallel -v --no-notice pip install {}
fi
if [ -f .travis.yml ]; then
echo "Found deps from travis:"
installs=$(grep 'pip install' .travis.yml | grep -v '\$' | sed -e 's/.*pip install/pip install/' | grep -v 'pip install . --use-mirrors' | sed -e 's/$/;/')
echo $installs
eval $installs
fi
deactivate
On OSX, brew kept refusing to link against its openssl with this error:
15:27 $ brew link --force openssl
Warning: Refusing to link: openssl
Linking keg-only openssl means you may end up linking against the insecure,
deprecated system OpenSSL while using the headers from Homebrew's openssl.
Instead, pass the full include/library paths to your compiler e.g.:
-I/usr/local/opt/openssl/include -L/usr/local/opt/openssl/lib
I finally was able to get it working with:
brew remove openssl
brew uninstall --force openssl
brew install openssl
export LDFLAGS=-L/usr/local/opt/openssl/lib
export CPPFLAGS=-I/usr/local/opt/openssl/include
brew remove python
brew update
brew install python
For Ubuntu
First check wheather install openssl-develop
sudo apt-get install libssl-dev
Try another way to reinstall pip
sudo apt-get install python-setuptools
sudo easy_install pip
use setuptools to install pip rather than install with source code may can solve the problem of dependency.
Just installed ssl pyopenssl
pip install pyopenssl
I compiled Python 2.6.6 with google-perf tools (tcmalloc) library to eliminate some of the memory issues I was having with the default 2.6.5. After getting 2.6.6 going it seems to not work becuase I think having issues with the default 2.6.5 install in Ubuntu. Will none of the binaries installed from the software channel like wxPython and setuptools work properly with 2.6.6. Do these need to be recompiled? Any other suggestions to get it working smoothly. Can I still set 2.6.5 as default without changing the Path? The path looks in usr/local/bin first.
A good general rule of thumb is to NEVER use the default system installed Python for any software development beyond miscellaneous system admin scripts. This applies on all UNIXes including Linux and OS/X.
Instead, build a good Python distro that you control, with the libraries (Python and C) that you need, and install this tarball in a non-system directory such as /opt/devpy or /data/package/python or /home/python. And why mess with 2.6 when 2.7.2 is available?
And when you are building it, make sure that all of its dependencies are in its own directory tree (RPATH) and that any system dependencies (.so files) are copied into its directory tree. Here is my version. It might not work if you just run the whole shell script. I always copy and paste sections of this into a terminal window and verify that each step worked OK. Make sure your terminal properties are set to allow lots of lines of scrollback, or only paste a couple of lines at a time.
(actually, after making a few tweaks I think this may be runnable as a script, however I would recommend something like ./pybuild.sh >pylog 2>&1 so you can comb through the output and verify that everything built OK.
This was built on Ubuntu 64 bit
#!/bin/bash
shopt -s compat40
export WGET=echo
#uncomment the following if you are running for the first time
export WGET=wget
sudo apt-get -y install build-essential
sudo apt-get -y install zlib1g-dev libxml2-dev libxslt1-dev libssl-dev libncurses5-dev
sudo apt-get -y install libreadline6-dev autotools-dev autoconf automake libtool
sudo apt-get -y install libsvn-dev mercurial subversion git-core
sudo apt-get -y install libbz2-dev libgdbm-dev sqlite3 libsqlite3-dev
sudo apt-get -y install curl libcurl4-gnutls-dev
sudo apt-get -y install libevent-dev libev-dev librrd4 rrdtool
sudo apt-get -y install uuid-dev libdb4.8-dev memcached libmemcached-dev
sudo apt-get -y install libmysqlclient-dev libexpat1-dev
cd ~
$WGET 'http://code.google.com/p/google-perftools/downloads/detail?name=google-perftools-1.7.tar.gz'
$WGET http://www.python.org/ftp/python/2.7.2/Python-2.7.2.tgz
tar zxvf Python-2.7.2.tgz
cd Python-2.7.2
#following is needed if you have an old version of Mercurial installed
#export HAS_HG=not-found
# To provide a uniform build environment
unset PYTHONPATH PYTHONSTARTUP PYTHONHOME PYTHONCASEOK PYTHONIOENCODING
unset LD_RUN_PATH LD_LIBRARY_PATH LD_DEBUG LD_TRACE_LOADED_OBJECTS
unset LD_PRELOAD SHLIB_PATH LD_BIND_NOW LD_VERBOSE
## figure out whether this is a 32 bit or 64 bit system
m=`uname -m`
if [[ $m =~ .*64 ]]; then
export CC="gcc -m64"
NBITS=64
elif [[ $m =~ .*86 ]]; then
export CC="gcc -m32"
NBITS=32
else # we are confused so bail out
echo $m
exit 1
fi
# some stuff related to distro independent build
# extra_link_args = ['-Wl,-R/data1/python27/lib']
#--enable-shared and a relative
# RPATH[0] (eg LD_RUN_PATH='${ORIGIN}/../lib')
export TARG=/data1/packages/python272
export TCMALLOC_SKIP_SBRK=true
#export CFLAGS='-ltcmalloc' # Google's fast malloc
export COMMONLDFLAGS='-Wl,-rpath,\$$ORIGIN/../lib -Wl,-rpath-link,\$$ORIGIN:\$$ORIGIN/../lib:\$$ORIGIN/../../lib -Wl,-z,origin -Wl,--enable-new-dtags'
# -Wl,-dynamic-linker,$TARG/lib/ld-linux-x86-64.so.2
export LDFLAGS=$COMMONLDFLAGS
./configure --prefix=$TARG --with-dbmliborder=bdb:gdbm --enable-shared --enable-ipv6
# if you have ia32-libs installed on a 64-bit system
#export COMMONLDFLAGS="-L/lib32 -L/usr/lib32 -L`pwd`/lib32 -Wl,-rpath,$TARG/lib32 -Wl,-rpath,$TARG/usr/lib32"
make
# ignore failure to build the following since they are obsolete or deprecated
# _tkinter bsddb185 dl imageop sunaudiodev
#install it and collect any dependency libraries - not needed with RPATH
sudo mkdir -p $TARG
sudo chown `whoami`.users $TARG
make install
# collect binary libraries ##REDO THIS IF YOU ADD ANY ADDITIONAL MODULES##
function collect_binary_libs {
cd $TARG
find . -name '*.so' | sed 's/^/ldd -v /' >elffiles
echo "ldd -v bin/python" >>elffiles
chmod +x elffiles
./elffiles | sed 's/.*=> //;s/ .*//;/:$/d;s/^ *//' | sort -u | sed 's/.*/cp -L & lib/' >lddinfo
# mkdir lib
chmod +x lddinfo
./lddinfo
cd ~
}
collect_binary_libs
#set the path
cd ~
export PATH=$TARG/bin:$PATH
#installed setuptools
$WGET http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg
chmod +x setuptools-0.6c11-py2.7.egg
./setuptools-0.6c11-py2.7.egg
#installed virtualenv
tar zxvf virtualenv-1.6.1.tar.gz
cd virtualenv-1.6.1
python setup.py install
cd ~
# created a base virtualenv that should work for almost all projects
# we make it relocatable in case its location in the filesystem changes.
cd ~
python virtualenv-1.6.1/virtualenv.py /data1/py27base # first make it
python virtualenv-1.6.1/virtualenv.py --relocatable /data1/py27base #then relocatabilize
# check it out
source ~/junk/bin/activate
python --version
# fill the virtualenv with useful modules
# watch out for binary builds that may have dependency problems
export LD_RUN_PATH='\$$ORIGIN:\$$ORIGIN/../lib:\$$ORIGIN/../../lib'
easy_install pip
pip install cython
pip install lxml
pip install httplib2
pip install python-memcached
pip install amqplib
pip install kombu
pip install carrot
pip install py_eventsocket
pip install haigha
# extra escaping of $ signs
export LDFLAGS='-Wl,-rpath,\$\$$ORIGIN/../lib:\$\$$ORIGIN/../../lib -Wl,-rpath-link,\$\$$ORIGIN/../lib -Wl,-z,origin -Wl,--enable-new-dtags'
# even more complex to build this one since we need some autotools and
# have to pull source from a repository
mkdir rabbitc
cd rabbitc
hg clone http://hg.rabbitmq.com/rabbitmq-codegen/
hg clone http://hg.rabbitmq.com/rabbitmq-c/
cd rabbitmq-c
autoreconf -i
make clean
./configure --prefix=/usr
make
sudo make install
cd ~
# for zeromq we get the latest source of the library
$WGET http://download.zeromq.org/zeromq-2.1.7.tar.gz
tar zxvf zeromq-2.1.7.tar.gz
cd zeromq-2.1.7
make clean
./configure --prefix=/usr
make
sudo make install
cd ~
# need less escaping of $ signs
export LDFLAGS='-Wl,-rpath,\$ORIGIN/../lib:\$ORIGIN/../../lib -Wl,-rpath-link,\$ORIGIN/../lib -Wl,-z,origin -Wl,--enable-new-dtags'
pip install pyzmq
pip install pylibrabbitmq # need to build C library and install first
pip install pylibmc
pip install pycurl
export LDFLAGS=$COMMONLDFLAGS
pip install cherrypy
pip install pyopenssl # might need some ldflags on this one?
pip install diesel
pip install eventlet
pip install fapws3
pip install gevent
pip install boto
pip install jinja2
pip install mako
pip install paste
pip install twisted
pip install flup
pip install pika
pip install pymysql
# pip install py-rrdtool # not on 64 bit???
pip install PyRRD
pip install tornado
pip install redis
# for tokyocabinet we need the latest source of the library
$WGET http://fallabs.com/tokyocabinet/tokyocabinet-1.4.47.tar.gz
tar zxvf tokyocabinet-1.4.47.tar.gz
cd tokyocabinet-1.4.47
make clean
./configure --prefix=/usr --enable-devel
make
sudo make install
cd ..
$WGET http://fallabs.com/tokyotyrant/tokyotyrant-1.1.41.tar.gz
tar zxvf tokyotyrant-1.1.41.tar.gz
cd tokyotyrant-1.1.41
make clean
./configure --prefix=/usr --enable-devel
make
sudo make install
cd ..
pip install tokyo-python
pip install solrpy
pip install pysolr
pip install sunburnt
pip install txamqp
pip install littlechef
pip install PyChef
pip install pyvb
pip install bottle
pip install werkzeug
pip install BeautifulSoup
pip install XSLTools
pip install numpy
pip install coverage
pip install pylint
# pip install PyChecker ???
pip install pycallgraph
pip install mkcode
pip install pydot
pip install sqlalchemy
pip install buzhug
pip install flask
pip install restez
pip install pytz
pip install mcdict
# need less escaping of $ signs
pip install py-interface
# pip install paramiko # pulled in by another module
pip install pexpect
# SVN interface
$WGET http://pysvn.barrys-emacs.org/source_kits/pysvn-1.7.5.tar.gz
tar zxvf pysvn-1.7.5.tar.gz
cd pysvn-1.7.5/Source
python setup.py backport
python setup.py configure
make
cd ../Tests
make
cd ../Sources
mkdir -p $TARG/lib/python2.7/site-packages/pysvn
cp pysvn/__init__.py $TARG/lib/python2.7/site-packages/pysvn
cp pysvn/_pysvn_2_7.so $TARG/lib/python2.7/site-packages/pysvn
cd ~
# pip install protobuf #we have to do this the hard way
$WGET http://protobuf.googlecode.com/files/protobuf-2.4.1.zip
unzip protobuf-2.4.1.zip
cd protobuf-2.4.1
make clean
./configure --prefix=/usr
make
sudo make install
cd python
python setup.py install
cd ~
pip install riak
pip install ptrace
pip install html5lib
pip install metrics
#redo the "install binary libraries" step
collect_binary_libs
# link binaries in the lib directory to avoid search path errors and also
# to reduce the number of false starts to find the library
for i in `ls $TARG/lib/python2.7/lib-dynload/*.so`
do
ln -f $i $TARG/lib/`basename $i`
done
# for the same reason link the whole lib directory to some other places in the tree
ln -s ../.. $TARG/lib/python2.7/site-packages/lib
# bundle it up and save it for packaging
cd /
tar cvf - .$TARG |gzip >~/py272-$NBITS.tar.gz
cd ~
# after untarring on another machine, we have a program call imports.py which imports
# every library as a quick check that it works. For a more positive check, run it like this
# strace -e trace=stat,fstat,open python imports.py >strace.txt 2>&1
# grep -v ' = -1' strace.txt |grep 'open(' >opens.txt
# sed <opens.txt 's/^open("//;s/".*//' |sort -u |grep -v 'dynload' |grep '\.so' >straced.txt
# ls -1d /data1/packages/python272/lib/* |sort -u >lib.txt
# then examine the strace output to see how many places it searches before finding it.
# a successful library load will be a call to open that doesn't end with ' = -1'
# If it takes too many tries to find a particular library, then another symbolic link may
# be a good idea
I'm pretty sure you have to compile wxPython to the version of Python that you want to use it with. That's always been the case with anyone else who has done something like this on the wxPython mailing list. I think that applies to most packages and especially so if they have any C/C++ components, like wxPython does. Pure Python packages can sometimes be transferred from one version to the next intact in my experience.
There are fairly extensive wxPython build instructions here: http://wxpython.org/BUILD-2.8.html
Robin Dunn and others on the wxPython mailing list are very helpful if you run into any problems.
If you compiled 2.6.6 and installed 2.6.5 from the repos, then ubuntu is having a conflict in finding what python you're using.
I'm flagging this to move to Superuser.