Instalação de módulos para Python3.3

Question

Estou tentando instalar o módulo biopython na minha máquina Ubuntu 12.04 LTS (64x). Primeiro fiz o upgrade para o Python3.3 instalando a partir do código-fonte (o biopython não suporta outras versões), isso parece ok.

No entanto, instalei alguns módulos usando o comando sudo apt-get install python-module , mas não consigo chamá-los de um shell python:

dovah@AsusX501A:~$ python3.3
Python 3.3.5 (default, Mar 12 2014, 02:09:17)
[GCC 4.6.3] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from biopython import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named 'biopython'
>>> from Bio import * ##as suggested in http://biopython.org/DIST/docs/api/module-tree.html
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named 'Bio'

Como você pode ver, os módulos estão instalados:

dovah@AsusX501A:~$ sudo apt-get install python-biopython
Reading package lists... Done
Building dependency tree      
Reading state information... Done
python-biopython is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

E o mesmo acontece com o biopython (bastante estranho: a linha 14 diz biopython-1.64-py2.7-linux-x86_64.egg , então o melhor hit foi encontrado para a versão 2.7 e não para a versão 3.3):

dovah@AsusX501A:~$ sudo easy_install -f http://biopython.org/DIST/ biopython
Searching for biopython
Reading http://biopython.org/DIST/
Best match: biopython 1.64
Downloading http://biopython.org/DIST/biopython-1.64.zip
Processing biopython-1.64.zip
Writing /tmp/easy_install-v5LJZz/biopython-1.64/setup.cfg
Running biopython-1.64/setup.py -q bdist_egg --dist-dir /tmp/easy_install-v5LJZz/biopython-1.64/egg-dist-tmp-TruGJH
warning: no previously-included files matching '.cvsignore' found under directory '*'
warning: no previously-included files matching '*.pyc' found under directory '*'
zip_safe flag not set; analyzing archive contents...
Bio.Entrez.Parser: module references __path__
Adding biopython 1.64 to easy-install.pth file
Installed /usr/local/lib/python2.7/dist-packages/biopython-1.64-py2.7-linux-x86_64.egg
Processing dependencies for biopython
Finished processing dependencies for biopython

São módulos específicos para uma determinada versão do Python? O sistema ainda está preso no Python 2.7? Obviamente, não posso simplesmente remover o 2.7, a menos que eu queira estragar meu sistema operacional inteiro.

Agradecemos antecipadamente por sua ajuda.

EDITAR numpy instalado com sucesso usando: sudo apt-get install python3-numpy

    

Answer 1

Funciona perfeitamente, confira. Primeiro comando:

sudo apt-get install python3-pip

Segundo comando:

pip3 install biopython

root@saurabh-ubuntu:/home/saurabh# apt-get install python-pip python3-pip
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  libexpat1-dev libpython3-dev libpython3.4-dev python-colorama python-distlib
  python-html5lib python-requests python-setuptools python-urllib3
  python3-colorama python3-dev python3-distlib python3-html5lib
  python3-setuptools python3.4-dev
Suggested packages:
  python-genshi
Recommended packages:
  python-dev-all
The following NEW packages will be installed:
  libexpat1-dev libpython3-dev libpython3.4-dev python-colorama python-distlib
  python-html5lib python-pip python-requests python-setuptools python-urllib3
  python3-colorama python3-dev python3-distlib python3-html5lib python3-pip
  python3-setuptools python3.4-dev
0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
Need to get 28.6 MB of archives.
After this operation, 48.0 MB of additional disk space will be used.
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Get:11 http://mirror.team-cymru.org/ubuntu/ trusty/universe python3-colorama all 0.2.5-0.1ubuntu1 [11.9 kB]
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root@saurabh-ubuntu:/home/saurabh# pip3 install biopython
Downloading/unpacking biopython
  Downloading biopython-1.64.tar.gz (11.7MB): 11.7MB downloaded
  Running setup.py (path:/tmp/pip_build_root/biopython/setup.py) egg_info for package biopython

    warning: no previously-included files matching '.cvsignore' found under directory '*'
    warning: no previously-included files matching '*.pyc' found under directory '*'
Installing collected packages: biopython
  Running setup.py install for biopython
    building 'Bio.cpairwise2' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-3.4/Bio/cpairwise2module.o
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/Bio/cpairwise2module.o -o build/lib.linux-x86_64-3.4/Bio/cpairwise2.cpython-34m.so
    building 'Bio.trie' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.4m -c Bio/triemodule.c -o build/temp.linux-x86_64-3.4/Bio/triemodule.o
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.4m -c Bio/trie.c -o build/temp.linux-x86_64-3.4/Bio/trie.o
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/Bio/triemodule.o build/temp.linux-x86_64-3.4/Bio/trie.o -o build/lib.linux-x86_64-3.4/Bio/trie.cpython-34m.so
    building 'Bio.Nexus.cnexus' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-3.4/Bio/Nexus/cnexus.o
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/Bio/Nexus/cnexus.o -o build/lib.linux-x86_64-3.4/Bio/Nexus/cnexus.cpython-34m.so

    warning: no previously-included files matching '.cvsignore' found under directory '*'
    warning: no previously-included files matching '*.pyc' found under directory '*'
Successfully installed biopython
Cleaning up...
root@saurabh-ubuntu:/home/saurabh# python3
Python 3.4.0 (default, Apr 11 2014, 13:05:11) 
[GCC 4.8.2] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> 
[3]+  Stopped                 python3
root@saurabh-ubuntu:/home/saurabh# 

    

Answer 2

Normalmente, python-* packages são direcionados para o Python 2.X. Os do Python 3 são denominados python3-* .

No seu caso, o pacote que você precisa não está disponível, então você precisará instalá-lo "manualmente".

Isso pode ser facilmente alcançado com o seguinte:

$ sudo apt-get install python3-dev python3-pip
$ sudo pip3 install biopython

Se você não quer que ele seja instalado em todo o sistema, você pode usar um virtualenv:

$ virtualenv -p python3.3 some_location  # replace 3.3 with your version. 
$ source some_location/bin/activate
$ pip install biopython # python3-dev should be already installed.