flo-compbio / xlmhg Goto Github PK
View Code? Open in Web Editor NEWXL-mHG: A Semiparametric Test for Enrichment in Ranked Lists.
Home Page: https://doi.org/10.7287/peerj.preprints.1962
License: BSD 3-Clause "New" or "Revised" License
xlmhg's Issues
A lot of tests fail on Windows
This is mostly due to hardcoded reference values, but may also include other problems.
Add Python 3.6 Windows builds once corresponding Cython binaries become available
Add p-value to title of plot.
Hi, I am using your algorithm to check for enrichment (at the top of the list). I currently am saving the item as a PNG and the can't get the p-vlaue to be part of the title... In addition, I am working with the png your provide from the website, is there any way to save the file in a different format ?(tiff)
any ides what I can do?
List length limit
Hi,
I see that the list length is restricted to 36536 but there is no information about this in the documentation. Why would you restrict the length of the list?
Thanks
mhg_cython in python 3.9 and above
Hello, thank you very much for developing xlmhg! I found a problem when using xlmhg in python above 3.8. The mhg_cython seems likely can be installed in python 3.9 but everything looks perfect in python 3.8.
Under python 3.9, I got warning:
Warning (xlmhg): Failed to import "mhg_cython" C extension.
Warning (xlmhg): Failed to import the "mhg_cython" C extension.Falling back to the pure Python implementation, which is very slow.
and I got error report if I run xlmhg testing:
File ~/miniconda3/envs/mebocost/lib/python3.9/site-packages/xlmhg/test.py:207, in get_xlmhg_test_result(N, indices, X, L, exact_pval, pval_thresh, escore_pval_thresh, table, use_alg1, tol)
201 raise ValueError('Supplied array for dynamic programming table not'
202 'large enough. It is: %d x %d, but must be at least '
203 '%d x %d ((K+1) x (W+1)).'
204 % (table.shape[0], table.shape[1], K+1, W+1))
206 ### Step 1: Calculate XL-mHG test statistic.
--> 207 stat, cutoff = mhg_cython.get_xlmhg_stat(indices, N, K, X, L, tol)
208 assert 0.0 <= stat <= 1.0
210 # check for special cases
TypeError: get_xlmhg_stat() takes from 3 to 4 positional arguments but 6 were given
Do you have any solution to this? Thank you very much!
Failing to build against python-numpy 1.23
xlmhg source from PyPi is failing to build against numpy version 1.23 with following error in archlinux
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/xlmhg
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fPIC -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c xlmhg/mhg_cython.c -o build/temp.linux-x86_64-cpython-310/xlmhg/mhg_cython.o
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from xlmhg/mhg_cython.c:599:
/usr/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
xlmhg/mhg_cython.c: In function ‘__pyx_tp_dealloc_array’:
xlmhg/mhg_cython.c:21202:5: error: lvalue required as increment operand
21202 | ++Py_REFCNT(o);
| ^~
xlmhg/mhg_cython.c:21204:5: error: lvalue required as decrement operand
21204 | --Py_REFCNT(o);
| ^~
xlmhg/mhg_cython.c: In function ‘__pyx_tp_dealloc_memoryview’:
xlmhg/mhg_cython.c:21513:5: error: lvalue required as increment operand
21513 | ++Py_REFCNT(o);
| ^~
xlmhg/mhg_cython.c:21515:5: error: lvalue required as decrement operand
21515 | --Py_REFCNT(o);
| ^~
xlmhg/mhg_cython.c: In function ‘__pyx_tp_dealloc__memoryviewslice’:
xlmhg/mhg_cython.c:21763:5: error: lvalue required as increment operand
21763 | ++Py_REFCNT(o);
| ^~
xlmhg/mhg_cython.c:21765:5: error: lvalue required as decrement operand
21765 | --Py_REFCNT(o);
| ^~
xlmhg/mhg_cython.c: In function ‘__Pyx_ParseOptionalKeywords’:
xlmhg/mhg_cython.c:23285:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23285 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from xlmhg/mhg_cython.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23285:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
23285 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23285:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23285 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23285:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23285 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23285:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
23285 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23285:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23285 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23301:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23301 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23301:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
23301 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23301:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23301 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23301:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23301 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23301:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
23301 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c:23301:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
23301 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
/usr/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
xlmhg/mhg_cython.c: In function ‘__Pyx_decode_c_string’:
xlmhg/mhg_cython.c:24439:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
24439 | return PyUnicode_FromUnicode(NULL, 0);
| ^~~~~~
/usr/include/python3.10/cpython/unicodeobject.h:551:42: note: declared here
551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
| ^~~~~~~~~~~~~~~~~~~~~
error: command '/usr/bin/gcc' failed with exit code 1Failed to build xlmhg
Hi,
To use COMETSC, I'm trying to install xlmhg 2.4.9, but got the error.
Could you kindly suggest what to do?
Thanks
Cython code fails to compile on Windows with Python 2.7 (Visual C++ 2008 / 9.0) due to `nanl`
The Visual C++ 2008 compiler does not know nanl (see here).
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