hichamjanati / mtw Goto Github PK
View Code? Open in Web Editor NEWWasserstein regularization for sparse multi-task regression
License: BSD 3-Clause "New" or "Revised" License
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proximal update
Hi, it seems the proximal update function is different from the paper. Line 48 in solver_cd.pyx shows:
z = theta - a - b
But in the paper the corresponding component in the derived proximal operator is:
z = theta - marginal*(b+1)
Hope you could help shed light on this.
Cheers,
Liu Peng
updage .gitingore
I get this:
(mtw-env) ❯ git status
On branch fix_more_ci
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git checkout -- <file>..." to discard changes in working directory)
modified: mtw/solver_cd.c
Untracked files:
(use "git add <file>..." to include in what will be committed)
doc/_build/
doc/auto_examples/
doc/generated/
mtw.egg-info/
maybe you should not track solver_cd.c and all the sphinx things need to be ignored
BUG: cannot import mtw because of "from ot import"
(mtw-env) ➜ mtw git:(master) ✗ python
Python 3.7.1 | packaged by conda-forge | (default, Nov 13 2018, 18:33:04)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from mtw import MTW
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/mathurin/workspace/mtw/mtw/__init__.py", line 1, in <module>
from .mtw import MTW
File "/home/mathurin/workspace/mtw/mtw/mtw.py", line 2, in <module>
from .solver import solver
File "/home/mathurin/workspace/mtw/mtw/solver.py", line 10, in <module>
from .otfunctions import (barycenterkl, barycenterkl_img, barycenterkl_log,
File "/home/mathurin/workspace/mtw/mtw/otfunctions.py", line 6, in <module>
from ot import emd2
ModuleNotFoundError: No module named 'ot'
@hichamjanati
What is ot supposed to be ?
Cython compilation errors
Hello -- thank you for making this project available.
I am running into some trouble trying to build and compile this:
(mtw) mtw (pep518)$pip install --no-deps -e .
WARNING: Missing build requirements in pyproject.toml for file:///Users/arokem/source/mtw.
WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.
open errors.tx ERROR: Command errored out with exit status 1:
command: /Users/arokem/.virtualenvs/mtw/bin/python3.7 /Users/arokem/.virtualenvs/mtw/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /var/folders/56/4s8_k8_s2n9c1622_bmnz7m40000gn/T/tmpjvb234qh
cwd: /Users/arokem/source/mtw
Complete output (1412 lines):
/private/var/folders/56/4s8_k8_s2n9c1622_bmnz7m40000gn/T/pip-build-env-w7qtokj_/overlay/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/arokem/source/mtw/mtw/solver_cd.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas/ddot.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas/dasum.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas/daxpy.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas/dnrm2.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas/dcopy.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport cython
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:6:0: 'scipy/linalg/cython_blas/dscal.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
from scipy.linalg.cython_blas cimport sdot, sasum, saxpy, snrm2, scopy, sscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:7:0: 'scipy/linalg/cython_blas/sdot.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
from scipy.linalg.cython_blas cimport sdot, sasum, saxpy, snrm2, scopy, sscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:7:0: 'scipy/linalg/cython_blas/sasum.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
from scipy.linalg.cython_blas cimport sdot, sasum, saxpy, snrm2, scopy, sscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:7:0: 'scipy/linalg/cython_blas/saxpy.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
from scipy.linalg.cython_blas cimport sdot, sasum, saxpy, snrm2, scopy, sscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:7:0: 'scipy/linalg/cython_blas/snrm2.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
from scipy.linalg.cython_blas cimport sdot, sasum, saxpy, snrm2, scopy, sscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:7:0: 'scipy/linalg/cython_blas/scopy.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
import numpy as np
from cython cimport floating
from libc.math cimport fabs, sqrt, fmax
from scipy.linalg.cython_blas cimport ddot, dasum, daxpy, dnrm2, dcopy, dscal
from scipy.linalg.cython_blas cimport sdot, sasum, saxpy, snrm2, scopy, sscal
^
------------------------------------------------------------
mtw/solver_cd.pyx:7:0: 'scipy/linalg/cython_blas/sscal.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
else:
return sdot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:23:15: 'sdot' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
else:
return sdot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:23:20: Cannot convert 'int *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
else:
return sdot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:23:23: Cannot convert 'float *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
else:
return sdot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:23:26: Cannot convert 'int *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
else:
return sdot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:23:32: Cannot convert 'float *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
else:
return sdot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:23:35: Cannot convert 'int *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return -1.0
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:21:15: 'ddot' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
return -1.0
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:21:20: Cannot convert 'int *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return -1.0
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:21:23: Cannot convert 'double *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return -1.0
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
^
------------------------------------------------------------
mtw/solver_cd.pyx:21:26: Cannot convert 'int *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
return -1.0
cdef floating fdot(int * n, floating * x, int * inc1, floating * y,
int * inc2) nogil:
if floating is double:
return ddot(n, x, inc1, y, inc2)
...
Unwanted files
There are files like .DS_blabla from macosx and .pyx that should not be there.
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