smsaladi/disembl

fork of DisEMBL (http://dis.embl.de/)

disembl's Issues

pip install egg_info/version error

pip fails to install dissemble package with differing errors depending on path of the command.

`➜ ~ cd disembl
➜ disembl git:(ctypes) ✗ ls
LICENSE README.md disembl setup.cfg setup.py test
➜ disembl git:(ctypes) ✗ pip install disembl
Collecting disembl
Could not find a version that satisfies the requirement disembl (from versions: )
No matching distribution found for disembl
➜ disembl git:(ctypes) ✗ pip install .
Processing /Users/annettebradbury/disembl
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "/var/folders/c_/t9xqhvhx52lg2y0nz3cstc1w0000gn/T/pip-egfff1u4-build/setup.py", line 1, in
gevent
NameError: name 'gevent' is not defined

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /var/folders/c_/t9xqhvhx52lg2y0nz3cstc1w0000gn/T/pip-egfff1u4-build/
➜ disembl git:(ctypes) ✗ `

Install fails from pypi or setuptools

Hi there!

Thanks for writing this package, I was about to do the same thing :)

I'd like to add this as a dependency for some software that we're putting together.
I can install it using the method that you describe in the readme and using pip:

pip install -e git+https://github.com/smsaladi/disembl.git

But if i try to install it from pypi (or using my setup.py script with the git repo linked) we get an error because it can't find include/russel.h

Would it be an enormous trouble to fix this path search error?

Below is the stack when i try to install from pypi (the setup.py script gives the same thing).

Cheers, Darcy

$ pip install disembl
Collecting disembl
Using cached disembl-2.0rc0.tar.gz
Building wheels for collected packages: disembl
Running setup.py bdist_wheel for disembl ... error
Complete output from command /home/darcy/projects/20170329-affectorp/env/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-5az2p34g/disembl/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/tmp0q096cblpip-wheel- --python-tag cp35:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/disembl
copying disembl/disembl.py -> build/lib.linux-x86_64-3.5/disembl
copying disembl/init.py -> build/lib.linux-x86_64-3.5/disembl
running build_ext
building 'disembl.libdisembl' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/disembl
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python3.5m -c disembl/libdisembl.c -o build/temp.linux-x86_64-3.5/disembl/libdisembl.o
disembl/libdisembl.c:30:28: fatal error: include/russel.h: No such file or directory
#include "include/russel.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1

---

Failed building wheel for disembl
Running setup.py clean for disembl
Failed to build disembl
Installing collected packages: disembl
Running setup.py install for disembl ... error
Complete output from command /home/darcy/projects/20170329-affectorp/env/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-5az2p34g/disembl/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-wt4yt6uh-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/darcy/projects/20170329-affectorp/env/include/site/python3.5/disembl:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/disembl
copying disembl/disembl.py -> build/lib.linux-x86_64-3.5/disembl
copying disembl/init.py -> build/lib.linux-x86_64-3.5/disembl
running build_ext
building 'disembl.libdisembl' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/disembl
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python3.5m -c disembl/libdisembl.c -o build/temp.linux-x86_64-3.5/disembl/libdisembl.o
disembl/libdisembl.c:30:28: fatal error: include/russel.h: No such file or directory
#include "include/russel.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/home/darcy/projects/20170329-affectorp/env/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-5az2p34g/disembl/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-wt4yt6uh-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/darcy/projects/20170329-affectorp/env/include/site/python3.5/disembl" failed with error code 1 in /tmp/pip-build-5az2p34g/disembl/

automating pytest

if you navigate into disembl/test, you can run py.test from that folder to run all the regression tests.

I think there is a way to have this integrated into setup.py, such that you can run a test command to have it build and test (without having to navigate to the test folder).

@nadinebradbury Can try to work this out? It will be useful for the ml-expression repo as well

DisEMBL error

Hello there,
I was able to install DisEMBL 2.0 by using pip, but when I am executing this error shows up.
DisEMBL.py 8 8 4 1.2 1.4 1.2 test/secy.faa scores
Traceback (most recent call last):
File "/home/rekhabohra/miniconda3/bin/DisEMBL.py", line 26, in
import disembl
File "/home/rekhabohra/miniconda3/lib/python3.6/site-packages/disembl/init.py", line 3, in
from .disembl import calc_disembl, default_params
File "/home/rekhabohra/miniconda3/lib/python3.6/site-packages/disembl/disembl.py", line 83
global libdisembl
^
SyntaxError: name 'libdisembl' is used prior to global declaration

Looking forward for solution.
Thank you in advance