Guide for developers

If you need to modify the algorithms/models in PaddleHelix, you have to switch to the developer mode. The core algorithms of PaddleHelix are mostly implemented in Python, but some also in C++, so you cannot develop PaddleHelix simply with pip install --editable {pahelix_path}. To develop on your machine, please do the following:

  • Please follow the Installation guide part to install all dependencies of PaddleHelix (paddlepaddle >= 2.0.0rc0, pgl >= 2.1).

  • If you have already installed distributed PaddleHelix with pip install paddlehelix, please uninstall it with:

$ pip uninstall paddlehelix

  • Clone this repository to your local machine, supposed path at /path_to_your_repo/:

$ git clone https://github.com/PaddlePaddle/PaddleHelix.git /path_to_your_repo/

$ cd /path_to_your_repo/

  • Depends on which model you’d like to modify, go to LinearRNA or Other algorithms:

    LinearRNA

    The source code of LinearRNA is at ./c/pahelix/toolkit/linear_rna/linear_rna. You could modify it for your needs. Then remember to return to the root directory of the repository, run scripts below to re-compile (please ensure there are cmake >= 3.6 and g++ >= 4.8 on your machine):

$ sh scripts/prepare.sh

$ sh scripts/build.sh

  • After a successful compilaiton, import LinearRNA as following:

$ cd build

$ python
>>> import c.pahelix.toolkit.linear_rna.linear_rna as linear_rna

  • Except LinearRNA, other algorithms in PaddleHelix are all implemented in Python.

    Other algorithms

    If you want to change these algorithms, just find and modify corresponding .py files under the path ./pahelix, then add /path_to_your_repo/ to your Python environment path:

import sys
sys.path.append('/path_to_your_repo/')
import pahelix

  • If you have any question or suggestion, feel free to file on our GitHub issue page. We will response ASAP.