gwas2vcf
py2many
gwas2vcf | py2many | |
---|---|---|
1 | 29 | |
39 | 599 | |
- | 2.5% | |
0.0 | 8.1 | |
about 1 year ago | about 1 month ago | |
Python | Python | |
MIT License | MIT License |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
gwas2vcf
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Nuitka: An extremely compatible Python compiler
Here is the original repo I have tried to speed up using:
python -m nuitka --clang --follow-imports main.py
repo: https://github.com/MRCIEU/gwas2vcf
If someone can make the program run faster by whatever means, it will make a bunch of people quite happy.
py2many
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Transpiler, a Meaningless Word
> Another problem is that there are hundreds of built-in library functions that need to be compiled from Python from C
An approach I've advocated as one of the main authors of py2many is that all of the python builtin functions be written in a subset of python[1] and then compiled into native code. This has the benefit of avoiding GIL, problems with C-API among other things.
Do checkout the examples here[2] which work out of the box for many of the 8-9 supported backends.
[1] https://github.com/py2many/py2many/blob/main/doc/langspec.md
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py2many VS kithon - a user suggested alternative
2 projects | 17 Jun 2023
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Why I'm still using Python
https://github.com/py2many/py2many/blob/main/doc/langspec.md
Reimplement a large enough, commonly used subset of python stdlib using this dialect and we may be in the business of writing cross platform apps (perhaps start with android and Ubuntu/Gnome)
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Codon: A high-performance Python compiler
For py2many, there is an informal specification here:
https://github.com/py2many/py2many/blob/main/doc/langspec.md
Would be great if all the authors of "python-like" languages get together and come up with a couple of specs.
I say a couple, because there are ones that support the python runtime (such as cython) and the ones which don't (like py2many).
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A Python-compatible statically typed language erg-lang/erg
It'd not fully solve your issue, but have you ever seen https://github.com/py2many/py2many ?
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Omyyyy/pycom: A Python compiler, down to native code, using C++
Cython doesn't consume python3 type hints and needs special type hints of its own. But it's certainly more mature than other players in the field.
What we need is a rpython suitable for app programming and a stdlib written in that dialect.
https://github.com/py2many/py2many/blob/main/doc/langspec.md
- I made a Python compiler, that can compile Python source down to fast, standalone executables.
- PyTorch: Where we are headed and why it looks a lot like Julia (but not exactly)
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Show HN: prometeo – a Python-to-C transpiler for high-performance computing
No intermediate AST. To understand the various stages of transpilation and separation of language specific and independent rewriters, this file is a good starting point:
https://github.com/adsharma/py2many/blob/main/py2many/cli.py...
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Implicit Overflow Considered Harmful (and how to fix it)
Link to the test that's relevant for this discussion:
https://github.com/adsharma/py2many/blob/main/tests/cases/in...
This is an explicit deviation from python's bigint, which doesn't map very well to systemsey languages. The next logical step is to build on this to have dependent and refinement types.
Work in progress here:
https://github.com/adsharma/Typpete
What are some alternatives?
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
pybind11 - Seamless operability between C++11 and Python
truvari - Structural variant toolkit for VCFs
PyO3 - Rust bindings for the Python interpreter
graalvm-ten-things - Top 10 Things To Do With GraalVM
PythonNet - Python for .NET is a package that gives Python programmers nearly seamless integration with the .NET Common Language Runtime (CLR) and provides a powerful application scripting tool for .NET developers.
pybenchmarks - Python Interpreters Benchmarks
PyCall.jl - Package to call Python functions from the Julia language
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
julia - The Julia Programming Language
Hail - Cloud-native genomic dataframes and batch computing
rust-numpy - PyO3-based Rust bindings of the NumPy C-API