Comments (5)
That's very confusing. It should look for numpy if it can run from numpy.distutils.misc_util import get_info
. Can you try running python3 -c "from numpy.distutils.misc_util import get_info; print('worked')"
? It should print "worked" in both cases.
from pybigwig.
Both on an install with numpy features enabled and disabled both print the same message:
python3 -c "from numpy.distutils.misc_util import get_info; print('worked')"
<string>:1: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
worked
Which is what I expected. I specifically made sure numpy was in the environment in both cases. Even if I run the python3 -m pip install -vv --upgrade --force-reinstall pybigwig
command with the additional --no-deps
option (and numpy already installed) to ensure nothing gets re-installed, it still fails to build with numpy
features enabled.
from pybigwig.
What happens if you run pip cache remove pyBigWig
before installing from pypi? I got it installed using numpy (numpy 1.23.3) in either case, but I wonder if it's just cached a build without numpy in your case.
from pybigwig.
You're correct. --force-reinstall
apparently still uses the cached pypi version. I had installed with pyBigWig as a dependency and it did not detect numpy which is its own issue. Force reinstalling apparently used the cached version built locally.
from pybigwig.
Caching is the cause of and solution to all of life's problems :P
from pybigwig.
Related Issues (20)
- RuntimeError: Invalid interval bounds
- Document performance considerations? HOT 4
- Cannot add entries of value type int, but only float HOT 2
- support for osx-arm64 HOT 2
- numpy support broken in 0.3.18? HOT 1
- Create a BedGraph file using addEntries() throws segmentation fault HOT 2
- library import error HOT 4
- Writing a nan value should leave a gap HOT 7
- Can't enforce numpy features when pyBigWig is used as a dependency in downstream package HOT 5
- pip installation broken HOT 4
- Installing through pip not working HOT 9
- addHeader does not support multiple calls HOT 1
- Support for python >=3.11 HOT 1
- Issue Downloading pyBigWig HOT 1
- Simple patch to resolve conflict with roundup() macro
- Stats Sum Not Working as Expected
- 'zsh: segmentation fault ' HOT 1
- Out of memory listing entries on one human chromosome on a machine with 300 GB ram and 165 GB BigBed file HOT 1
- pyBigWig.entries() should return empty array, not None when no entries are found
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 pybigwig.