Comments (5)
#162 looks like it might be related to this issue. The cython/C functions
_cross_correlation_max()
/_cross_correlation_max_fast()
and
_cross_correlation_all()
/_cross_correlation_all_fast()
used in CouplingAnalyis
should therefore be looked into as well.
from pyunicorn.
The test suite passes on the freshly installed master
branch for me, hence I am unable to reproduce this issue at the moment. You might want to look at my recent commits touching these files and see if reverting them changes your situation: 6dc0f63, 402197f, 21b0b6f. For example, if reverting the third commit resolved your issue, then that might indicate a platform-specific problem with the ALLOCA
macro defined there.
funcnet/_ext/src_numerics.c::_get_nearest_neighbors_fast()
is the last function in that file which has not been Cythonized yet. It would be great if you could port it, examine the remaining C functions (compare them against the legacy Weave code in the original commits and the current Cython versions), and delete the C file.
from pyunicorn.
That's curious. I did a fresh install on a new conda environment and still get the segfaults wenn running the test suite via tox.
I admit my system is not the latest, running on macOS 10.13, not sure if that might be a problem. I still have a conda=23.3 and python=3.10 though.
I could not do full reverts of the above commits because that breaks the cython compilation on reinstall, so I tried reverting only changes concerning funcnet
(including setup.py
and core/_ext/types.{pxd|py}
) for all the above commits:
which all compiled fine, but didn't fix the segfault.
I also tried python 3.9 and 3.11 but no difference. (won't install on python=3.8 because numpy=1.25 needs python>=3.9)
Any more ideas at this point? Otherwise I will try porting funcnet/_ext/src_numerics.c::_get_nearest_neighbors_fast()
to cython and see if that fixes it.
Thanks for the hint by the way, didn't realize funcnet/_ext/src_numerics.c::_cross_correlation_{max|all}_fast()
were unused. _symmetrize_by_absmax_fast()
is also still in there though.
from pyunicorn.
This sounds like a bug whose manifestation is compiler/platform-dependent. Cythonizing would therefore probably be of comparable effort to debugging the C version, and reducing the language diversity would be beneficial independently of fixing this bug. Sorry, I overlooked _symmetrize_by_absmax_fast()
, but the same reasoning applies for it.
I fixed the Numpy issue in a9a70b2.
from pyunicorn.
Thanks for fixing the numpy issue! Will look into cythonizing the remaining C functions for CouplingAnalysis
as soon as possible.
from pyunicorn.
Related Issues (20)
- LINT: few remaining refactor and warning flags to be resolved HOT 2
- Tests failing with `Unable to lock file`
- pip install pyunicorn error:error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\Community\\VC\\Tools\\MSVC\\14.29.30133\\bin\\HostX86\\x64\\cl.exe' failed with exit code 2 HOT 1
- LINT: disabled `pylint` flags should be re-enabled where possible, or disabled locally HOT 5
- Replace: `progressbar` -> `tqdm`
- MAINT: add `cython-lint` to test suite
- MAINT: review funcionality and use of `CouplingAnalysis.get_nearest_neighbors()` and add a specific test
- ENH: Theiler window option for diagonal RQA measures in `RecurrencePlot` HOT 2
- CI: set up Travis CI for macOS and Windows builds
- MAINT: drop `climate.MapPlots` in favour of `climate.CartopyPlots` HOT 2
- ENH: Remove old examples folder
- `Network.nsi_local_clustering()` might encounter divide by zero when `typical_weight` is given HOT 1
- module 'numpy' has no attribute 'int' HOT 1
- Failed building wheel for pyunicorn while installing HOT 4
- Printing `ClimateData` object throws `KeyError` from `h5netcdf` HOT 2
- Add `typical_weight` argument for all n.s.i. measures to enable their "corrected" versions
- numpy module not found during installation (Win10) HOT 1
- DOC: sphinx `Didn't find <class attribute> in <module>` when building docs HOT 2
- ModuleNotFoundError from pip install (version 0.6.1) HOT 2
- Complete implementation of new caching system, and extend
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pyunicorn.