Comments (11)
The code is there :-( it apparently hasn't built for you? What did setup.py install say for you when you ran it? Did it complain about anything?
from umap.
It said some things :)
running install
running bdist_egg
running egg_info
creating umap.egg-info
writing requirements to umap.egg-info/requires.txt
writing umap.egg-info/PKG-INFO
writing top-level names to umap.egg-info/top_level.txt
writing dependency_links to umap.egg-info/dependency_links.txt
writing manifest file 'umap.egg-info/SOURCES.txt'
reading manifest file 'umap.egg-info/SOURCES.txt'
writing manifest file 'umap.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.6-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-10.6-x86_64-2.7
creating build/lib.macosx-10.6-x86_64-2.7/umap
copying umap/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/umap
copying umap/umap_.py -> build/lib.macosx-10.6-x86_64-2.7/umap
running build_ext
cythoning umap/umap_utils.pyx to umap/umap_utils.c
building 'umap.umap_utils' extension
creating build/temp.macosx-10.6-x86_64-2.7
creating build/temp.macosx-10.6-x86_64-2.7/umap
gcc -fno-strict-aliasing -I/Users/max/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include -I/usr/include -I/Users/max/anaconda/include/python2.7 -c umap/umap_utils.c -o build/temp.macosx-10.6-x86_64-2.7/umap/umap_utils.o
In file included from umap/umap_utils.c:274:
In file included from /Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:
/Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning:
"Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API
NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from umap/umap_utils.c:274:
In file included from /Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:
/Users/max/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1453:1: warning:
unused function '_import_array' [-Wunused-function]
_import_array(void)
^
umap/umap_utils.c:28421:32: warning: unused function '__Pyx_PyUnicode_FromString'
[-Wunused-function]
static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
^
umap/umap_utils.c:367:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function]
static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
^
umap/umap_utils.c:24646:32: warning: unused function '__Pyx_GetItemInt_List_Fast'
[-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
^
umap/umap_utils.c:24661:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast'
[-Wunused-function]
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
^
umap/umap_utils.c:25059:1: warning: unused function '__pyx_add_acquisition_count_locked'
[-Wunused-function]
__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
^
umap/umap_utils.c:25069:1: warning: unused function '__pyx_sub_acquisition_count_locked'
[-Wunused-function]
__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
^
umap/umap_utils.c:26662:46: warning: unused function '__Pyx_PyInt_From_npy_int8' [-Wunused-function]
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int8(npy_int8 value) {
^
umap/umap_utils.c:26725:48: warning: unused function '__pyx_t_float_complex_from_parts'
[-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
^
umap/umap_utils.c:26736:30: warning: unused function '__Pyx_c_eqf' [-Wunused-function]
static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
^
umap/umap_utils.c:26739:48: warning: unused function '__Pyx_c_sumf' [-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t...
^
umap/umap_utils.c:26745:48: warning: unused function '__Pyx_c_difff' [-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_...
^
umap/umap_utils.c:26757:48: warning: unused function '__Pyx_c_quotf' [-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_...
^
umap/umap_utils.c:26764:48: warning: unused function '__Pyx_c_negf' [-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
^
umap/umap_utils.c:26770:30: warning: unused function '__Pyx_c_is_zerof' [-Wunused-function]
static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
^
umap/umap_utils.c:26773:48: warning: unused function '__Pyx_c_conjf' [-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
^
umap/umap_utils.c:26787:52: warning: unused function '__Pyx_c_powf' [-Wunused-function]
static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __p...
^
umap/umap_utils.c:26847:49: warning: unused function '__pyx_t_double_complex_from_parts'
[-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, ...
^
umap/umap_utils.c:26858:30: warning: unused function '__Pyx_c_eq' [-Wunused-function]
static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
^
umap/umap_utils.c:26861:49: warning: unused function '__Pyx_c_sum' [-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_...
^
umap/umap_utils.c:26867:49: warning: unused function '__Pyx_c_diff' [-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx...
^
umap/umap_utils.c:26879:49: warning: unused function '__Pyx_c_quot' [-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx...
^
umap/umap_utils.c:26886:49: warning: unused function '__Pyx_c_neg' [-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
^
umap/umap_utils.c:26892:30: warning: unused function '__Pyx_c_is_zero' [-Wunused-function]
static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
^
umap/umap_utils.c:26895:49: warning: unused function '__Pyx_c_conj' [-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
^
umap/umap_utils.c:26909:53: warning: unused function '__Pyx_c_pow' [-Wunused-function]
static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __...
^
umap/umap_utils.c:27422:45: warning: function '__Pyx_PyInt_As_npy_int8' is not needed and will not
be emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE npy_int8 __Pyx_PyInt_As_npy_int8(PyObject *x) {
^
umap/umap_utils.c:27792:41: warning: function '__Pyx_PyInt_As_char' is not needed and will not be
emitted [-Wunneeded-internal-declaration]
static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) {
^
umap/umap_utils.c:9307:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew1'
[-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) {
^
umap/umap_utils.c:9354:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew2'
[-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyO...
^
umap/umap_utils.c:9401:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew3'
[-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyO...
^
umap/umap_utils.c:9448:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew4'
[-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyO...
^
umap/umap_utils.c:9495:32: warning: unused function '__pyx_f_5numpy_PyArray_MultiIterNew5'
[-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyO...
^
umap/umap_utils.c:10297:27: warning: unused function '__pyx_f_5numpy_set_array_base'
[-Wunused-function]
static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObjec...
^
umap/umap_utils.c:10393:32: warning: unused function '__pyx_f_5numpy_get_array_base'
[-Wunused-function]
static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) {
^
36 warnings generated.
gcc -bundle -undefined dynamic_lookup -L/Users/max/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.6-x86_64-2.7/umap/umap_utils.o -L/usr/lib -L/Users/max/anaconda/lib -lgsl -lcblas -o build/lib.macosx-10.6-x86_64-2.7/umap/umap_utils.so
creating build/bdist.macosx-10.6-x86_64
creating build/bdist.macosx-10.6-x86_64/egg
creating build/bdist.macosx-10.6-x86_64/egg/umap
copying build/lib.macosx-10.6-x86_64-2.7/umap/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/umap
copying build/lib.macosx-10.6-x86_64-2.7/umap/umap_.py -> build/bdist.macosx-10.6-x86_64/egg/umap
copying build/lib.macosx-10.6-x86_64-2.7/umap/umap_utils.so -> build/bdist.macosx-10.6-x86_64/egg/umap
byte-compiling build/bdist.macosx-10.6-x86_64/egg/umap/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/umap/umap_.py to umap_.pyc
creating stub loader for umap/umap_utils.so
byte-compiling build/bdist.macosx-10.6-x86_64/egg/umap/umap_utils.py to umap_utils.pyc
creating build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying umap.egg-info/PKG-INFO -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying umap.egg-info/SOURCES.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying umap.egg-info/dependency_links.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying umap.egg-info/requires.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying umap.egg-info/top_level.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
writing build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/umap-0.0.1-py2.7-macosx-10.6-x86_64.egg' and adding 'build/bdist.macosx-10.6-x86_64/egg' to it
removing 'build/bdist.macosx-10.6-x86_64/egg' (and everything under it)
Processing umap-0.0.1-py2.7-macosx-10.6-x86_64.egg
Removing /Users/max/anaconda/lib/python2.7/site-packages/umap-0.0.1-py2.7-macosx-10.6-x86_64.egg
Copying umap-0.0.1-py2.7-macosx-10.6-x86_64.egg to /Users/max/anaconda/lib/python2.7/site-packages
umap 0.0.1 is already the active version in easy-install.pth
Installed /Users/max/anaconda/lib/python2.7/site-packages/umap-0.0.1-py2.7-macosx-10.6-x86_64.egg
Processing dependencies for umap==0.0.1
Searching for Cython==0.24.1
Best match: Cython 0.24.1
Adding Cython 0.24.1 to easy-install.pth file
Using /Users/max/anaconda/lib/python2.7/site-packages
Searching for scikit-learn==0.18
Best match: scikit-learn 0.18
Adding scikit-learn 0.18 to easy-install.pth file
Using /Users/max/anaconda/lib/python2.7/site-packages
Finished processing dependencies for umap==0.0.1
from umap.
That all looks ... fine. I was hoping it would have something informatively weird. It did specifically say it built umap_utils, so now I'm confused as to why it isn't there for you. I wish I actually understood how python packaging works.
from umap.
If you can do a
python setup.py build
And then cd into the appropriate directory and run from there that might work ... and if it doesn't we can maybe diagnose why a little easier. I don't know how to debug egg files.
from umap.
Ran above and upgraded to the versions in your tweet. Is it saying skipping imap_utils.c here a clue?
python setup.py build
running build
running build_py
copying umap/umap_.py -> build/lib.macosx-10.6-x86_64-2.7/umap
running build_ext
skipping 'umap/umap_utils.c' Cython extension (up-to-date)```
from umap.
No, that should be fine (it's already, in principle) built it. Ideally in build/lib.macosx-10.6-x86_64-2.7/umap there should be a file umap_utils.cpython-35m-darwin.so (or similarly named; perhaps with a 27 instead of 35). If that isn't there then that's the problem ... if it is then try:
cd build/lib.macosx-10.6-x86_64-2.7
python
>>> import umap
because that should work if the file is there. This may be a python2/python3 thing where I haven't gotten compatability in local package referencing. I'll look into that now, but I'm about to board a flight, so might not be able to update for several hours.
from umap.
The file is there – and the import from that folder works! Thanks for your great work and time.
from umap.
Still not sure why the install doesn't work, but hopefully that can be ironed out at a later date.
from umap.
same problem for me (and same "solution"). Built with miniconda.
from umap.
I'll see what I can figure out, but I admit I am completely at a loss right now. Sorry. At least there is a workaround, just not a good one.
from umap.
Seems to be resolved in current version.
from umap.
Related Issues (20)
- Implementation of sciki-learn's get_feature_names_out() API is not correct
- Is 'n_training_epochs' working for parameteric UMAP?
- visualize video data
- How to combine UMAP models in new data?
- Edit instructions to make them compatible with zsh
- Empty API page on UMAP API Guide? HOT 1
- PCA diagnostic error HOT 2
- Speed inquries HOT 2
- UMAP crashes when torch also imported before first run HOT 2
- Unable to pickle trained UMAP instance
- Reducing Model Size for UMAP on Large Datasets HOT 2
- umap.UMAP accepts strings as n_neighbors and min_dist, causing later failures
- Optimal dimensions
- RunUMAP Failing HOT 1
- Semi-deterministic output even though randon_state is set
- TypeError: Dispatcher._rebuild() got an unexpected keyword argument 'impl_kind' HOT 1
- illegal hardware instruction python HOT 2
- Transform new input with composite model HOT 1
- Inquiry on Utilizing UMAP for Text Similarity and Clustering HOT 4
- No clear documentation of default parameter values HOT 1
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from umap.