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CONTRIBUTING.md

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Contribute to cuCIM

If you are interested in contributing to cuCIM, your contributions will fall into three categories:

  1. You want to report a bug, feature request, or documentation issue
    • File an issue describing what you encountered or what you want to see changed.
    • The RAPIDS team will evaluate the issues and triage them, scheduling them for a release. If you believe the issue needs priority attention comment on the issue to notify the team.
  2. You want to propose a new Feature and implement it
    • Post about your intended feature, and we shall discuss the design and implementation.
    • Once we agree that the plan looks good, go ahead and implement it, using the code contributions guide below.
  3. You want to implement a feature or bug-fix for an outstanding issue
    • Follow the code contributions guide below.
    • If you need more context on a particular issue, please ask and we shall provide.

Code contributions

Your first issue

  1. Read the project's README.md to learn how to setup the development environment
  2. Find an issue to work on. The best way is to look for the good first issue or help wanted labels
  3. Comment on the issue saying you are going to work on it
  4. Code! Make sure to update unit tests!
  5. When done, create your pull request
  6. Verify that CI passes all status checks. Fix if needed
  7. Wait for other developers to review your code and update code as needed
  8. Once reviewed and approved, a RAPIDS developer will merge your pull request

Remember, if you are unsure about anything, don't hesitate to comment on issues and ask for clarifications!

Seasoned developers

Once you have gotten your feet wet and are more comfortable with the code, you can look at the prioritized issues of our next release in our project boards.

Pro Tip: Always look at the release board with the highest number for issues to work on. This is where RAPIDS developers also focus their efforts.

Look at the unassigned issues, and find an issue you are comfortable with contributing to. Start with Step 3 from above, commenting on the issue to let others know you are working on it. If you have any questions related to the implementation of the issue, ask them in the issue instead of the PR.

Setting Up Your Build Environment

The following instructions are for developers and contributors to cuCIM OSS development. These instructions are tested on Linux Ubuntu 16.04 & 18.04. Use these instructions to build cuCIM from source and contribute to its development. Other operating systems may be compatible, but are not currently tested.

Code Formatting

Python

cuCIM uses isort, and flake8 to ensure a consistent code format throughout the project. isort, and flake8 can be installed with conda or pip:

conda install isort flake8
pip install isort flake8

These tools are used to auto-format the Python code in the repository. Additionally, there is a CI check in place to enforce that committed code follows our standards. You can use the tools to automatically format your python code by running:

isort --atomic python/**/*.py

Get libcucim Dependencies

Compiler requirements:

  • gcc version 9.0+
  • nvcc version 11.0+
  • cmake version 3.18.0+

CUDA/GPU requirements:

  • CUDA 11.0+
  • NVIDIA driver 450.36+
  • Pascal architecture or better

You can obtain CUDA from https://developer.nvidia.com/cuda-downloads.

Script to build cuCIM from source

Build from Source

  • Clone the repository
CUCIM_HOME=$(pwd)/cucim
git clone https://github.com/rapidsai/cucim.git $CUCIM_HOME
cd $CUCIM_HOME
  • Create the conda development environment cucim:
conda env create -f ./conda/environments/env.yml
# activate the environment
conda activate cucim
  • Build and install libcucim and cucim (python bindings):
export CC=$CONDA_PREFIX/bin/x86_64-conda_cos6-linux-gnu-gcc
export CXX=$CONDA_PREFIX/bin/x86_64-conda_cos6-linux-gnu-g++
./run build_local all release $CONDA_PREFIX

  • Build command will create the following files:

    • ./install/lib/libcucim*
    • ./python/install/lib/_cucim.cpython-38-x86_64-linux-gnu.so
    • ./cpp/plugins/cucim.kit.cuslide/install/lib/cucim.kit.cuslide@*.so

  • Install libcucim/cuslide/cucim(python):

# libcucim
cp -P -r install/bin/* $CONDA_PREFIX/bin/
cp -P -r install/lib/* $CONDA_PREFIX/lib/
cp -P -r install/lib/* $CONDA_PREFIX/lib/
cp -P -r install/include/* $CONDA_PREFIX/include/

# cuslide plugin
cp -P -r cpp/plugins/cucim.kit.cuslide/install/bin/* $CONDA_PREFIX/bin
cp -P -r cpp/plugins/cucim.kit.cuslide/install/lib/* $CONDA_PREFIX/lib/

# cucim (python)
cp -P python/install/lib/* python/cucim/src/cucim/clara/
cd python/cucim/
python -m pip install .