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‎.github/ISSUE_TEMPLATE/01-bug-report.md‎

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---
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name: 🐛 Bug
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about: Report a problem
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labels: 'bug'
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---
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## Problem
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> A report of the problem you observed.
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## Expectation
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> A description of what you were expecting to observe instead.
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## Suggestion
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> Some ideas about how to solve that problem.
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## Reproducibility
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> Steps to reproduce your observations so we can see the problem too, ideally some minimal code example.
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## Additional context
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> More context about your project, operating system, hardware or whatever to better understand the issue.

‎.github/ISSUE_TEMPLATE/02-trajectory-request.md‎

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---
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name: 🎇 Trajectory request
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about: Propose a new trajectory for MRI-nufft
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labels: ['trajectories', 'feature request']
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title: "Add trajectory"
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---
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## The trajectory
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> Describe the trajectory/sampling pattern, don't hesitate to add pictures.
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## References
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> Add publication and/or code references.

‎.github/ISSUE_TEMPLATE/03-installation-trouble.md‎

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---
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name: 🛠️ Installation issues
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about: Failed to install MRI-nufft or one of its backend ?
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title: "Installation issue with "
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---
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<!-- Please fill out the following sections to help us understand your issue.
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Before submitting, please ensure that you have read the installation guidelines:
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https://mind-inria.github.io/mri-nufft/getting_started.html
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-->
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## My System
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- **OS**: [e.g. Ubuntu 20.04, macOS 11.2, Windows 10]
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- **Python version**: [e.g. 3.8.5]
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- **CUDA version**: [if applicable, e.g. 11.2]
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- **package manager** [e.g. pip, uv, conda]
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## What I did
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> Describe the steps you took to install MRI-nufft or its backend, including any commands you ran.
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## What happened
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> Describe the error messages or issues you encountered during installation.
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> If possible, include the full output of the installation command.
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## Additional context
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> Provide any additional information that might help diagnose the issue.

‎.github/ISSUE_TEMPLATE/04-feature-request.md‎

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---
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name: ✨ Feature request
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about: Suggest a new feature for MRI-nufft
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labels: 'feature request'
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---
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## Description & use cases
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> Describe the feature you would like to see in MRI-nufft. Be as specific as possible about what you want to achieve.
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## Suggested implementation
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> Describe how you envision the feature being implemented. This could include specific functions, classes, or changes to existing code.

‎.github/pull_request_template.md‎

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<!---
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This is a suggested pull request template for mri-nufft.
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It's designed to capture information we've found to be useful in reviewing pull requests.
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If there is other information that would be helpful to include, please don't hesitate to add it!
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Please make sure your pull request also follows the
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[contribution guidelines](https://github.com/mind-inria/mri-nufft/blob/master/CONTRIBUTING.md) that
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will be enforced during the review process.
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-->
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<!-- Please indicate after the # which issue you're closing with this PR.
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This is helpful for the maintainers AND will magically close the issue when this
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pull request is merged!
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If the PR closes multiple issues, includes "closes" before each one is listed.
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https://help.github.com/articles/closing-issues-using-keywords -->
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- Closes #
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<!-- Please give a brief overview of what has changed in the PR.
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If you're not sure what to write, consider it a note to the maintainers to indicate
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what they should be looking for when they review the pull request. -->
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Changes proposed in this pull request:
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-
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-

‎.github/workflows/test-ci.yml‎

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${{ env.create_venv }}
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${{ env.activate_venv }}
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python -m pip install --upgrade pip
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python -m pip install -e .[test]
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- name: Install pynfft
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if: ${{ matrix.backend == 'pynfft' || env.ref_backend == 'pynfft' }}
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shell: bash
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run: |
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${{ env.activate_venv }}
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python -m pip install "pynfft2>=1.4.3"
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- name: Install pynufft
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if: ${{ matrix.backend == 'pynufft-cpu' || env.ref_backend == 'pynufft-cpu' }}
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run: |
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${{ env.activate_venv }}
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python -m pip install pynufft
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- name: Install finufft
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if: ${{ matrix.backend == 'finufft' || env.ref_backend == 'finufft'}}
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shell: bash
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run: |
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${{ env.activate_venv }}
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python -m pip install finufft
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- name: Install Sigpy
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if: ${{ matrix.backend == 'sigpy' || env.ref_backend == 'sigpy'}}
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shell: bash
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run: |
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${{ env.activate_venv }}
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python -m pip install sigpy
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- name: Install BART
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python -m pip install -e .[test,${{ env.ref_backend }},${{ matrix.backend }}]
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- name: Install BART if needed
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if: ${{ matrix.backend == 'bart' || env.ref_backend == 'bart'}}
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shell: bash
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run: |
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make
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echo $PWD >> $GITHUB_PATH
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- name: Install torchkbnufft-cpu
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if: ${{ matrix.backend == 'torchkbnufft-cpu' || env.ref_backend == 'torchkbnufft-cpu'}}
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run: |
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${{ env.activate_venv }}
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python -m pip install torchkbnufft
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- name: Run Tests
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shell: bash
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- name: Install mri-nufft and finufft
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shell: bash
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run: |
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${{ env.create_venv }}
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${{ env.activate_venv }}
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python -m pip install --upgrade pip wheel
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python -m pip install -e .[test]
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python -m pip install cupy-cuda12x finufft "numpy<2.0"
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cd $RUNNER_WORKSPACE
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python --version
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python -m venv venv
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source $RUNNER_WORKSPACE/venv/bin/activate
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pip install --upgrade pip wheel
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pip install -e mri-nufft[test,finufft]
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- name: Install torch with CUDA 12.1
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shell: bash
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if: ${{ matrix.backend != 'tensorflow'}}
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run: |
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${{ env.activate_venv }}
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${{ env.setup_cuda }}
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python -m pip install torch
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- name: Install backend
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shell: bash
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run: |
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${{ env.activate_venv }}
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if [[ ${{ matrix.backend }} == "torchkbnufft-gpu" ]]; then
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python -m pip install torchkbnufft
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elif [[ ${{ matrix.backend }} == "tensorflow" ]]; then
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python -m pip install tensorflow-mri==0.21.0 tensorflow-probability==0.17.0 tensorflow-io==0.27.0 matplotlib==3.7
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elif [[ ${{ matrix.backend }} == "cufinufft" ]]; then
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python -m pip install "cufinufft<2.3"
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else
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python -m pip install ${{ matrix.backend }}
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fi
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source $RUNNER_WORKSPACE/venv/bin/activate
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export CUDA_BIN_PATH=/usr/local/cuda-12.4/
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export PATH=/usr/local/cuda-12.4/bin/:${PATH}
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export LD_LIBRARY_PATH=/usr/local/cuda-12.4/lib64/:${LD_LIBRARY_PATH}
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pip install -e .[${{ matrix.backend }},autodiff]
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- name: Run Tests
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shell: bash
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${{ env.activate_venv }}
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python -m pip install --upgrade pip
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python -m pip install -e .[extra,test,dev]
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python -m pip install finufft pooch brainweb-dl torch fastmri
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python -m pip install pooch brainweb-dl torch fastmri
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- name: Install GPU related interfaces
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- name: Install Python deps
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shell: bash
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${{ env.activate_venv }}
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${{ env.setup_cuda }}
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pip install cupy-cuda12x torch
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python -m pip install gpuNUFFT "cufinufft<2.3" sigpy scikit-image fastmri
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python -m pip install --upgrade pip
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python -m pip install -e .[test,dev,finufft,cufinufft,gpuNUFFT,sigpy,smaps,autodiff,doc]
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- name: Run examples
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${{ env.activate_venv }}
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export COVERAGE_FILE=coverage_plots
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export MRINUFFT_BACKEND=cufinufft
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python -m pytest examples -n=4 --cov --cov-branch --cov-report=term --durations=10
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- name: Cache brainweb-dl directory
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uses: actions/setup-python@v5
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with:
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- name: Point to CUDA 12.4
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run: |
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export CUDA_BIN_PATH=/usr/local/cuda-12.4/
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export PATH=/usr/local/cuda-12.4/bin/:${PATH}
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export LD_LIBRARY_PATH=/usr/local/cuda-12.4/lib64/:${LD_LIBRARY_PATH}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install .[doc,extra]
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python -m pip install finufft
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- name: Install GPU related interfaces
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run: |
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${{ env.activate_venv }}
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${{ env.setup_cuda }}
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pip install cupy-cuda12x torch
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python -m pip install gpuNUFFT "cufinufft<2.3" sigpy scikit-image fastmri
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python -m pip install .[doc,finufft,autodiff,gpunufft,cufinufft,sigpy,extra] fastmri
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- name: Build API documentation
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export MRINUFFT_BACKEND=cufinufft
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python -m sphinx docs docs_build
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- name: Display data

‎CONTRIBUTING.md‎

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cd mri-nufft/docs
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cd ..
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# you can specify a specfic backend to run the example with an environment variable:
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export MRINUFFT_BACKEND=finufft
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python -m sphinx-build docs docs_build
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python -m http.server --directory docs_build 8080
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## Styleguides
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### Code
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The code base is formatted with [`black`](https://github.com/psf/black) and style guide is enforced with [`ruff`](https://github.com/astral-sh/ruff). You can run `black .` and `ruff check src` to ensure your changes will pass the [linter-check](https://github.com/mind-inria/.github/workflows/style.yml) CI.
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### Docstrings
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We use Numpy style docstrings. You can find more information about them [here](https://numpydoc.readthedocs.io/en/latest/format.html).
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‎README.rst‎

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## The real deal starts here ##
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# Choose your NUFFT backend (installed independently from the package)
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# pip install mri-nufft[finufft] will be just fine here
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NufftOperator = mrinufft.get_operator("finufft")
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# For improved image reconstruction, use density compensation
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Additionally, you will have to install at least one NUFFT computation backend. See the `Documentation <https://mind-inria.github.io/mri-nufft/getting_started.html#choosing-a-nufft-backend>`_ for more guidance.
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Typically we recommend::
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pip install mri-nufft[finufft]
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pip install mri-nufft[cufinufft] # if you have a NVIDIA GPU and CUDA>=12
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Benchmark

‎docs/_templates/autosummary/class.rst‎

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{%- endfor %}
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{% endif %}
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{% endblock %}
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.. _sphx_glr_backref_{{fullname}}:
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.. minigallery:: {{fullname}}
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:add-heading:

‎docs/_templates/autosummary/function.rst‎

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.. autofunction:: {{ objname }}
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.. _sphx_glr_backref_{{fullname}}:
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.. minigallery:: {{fullname}}
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:add-heading:
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.. minigallery:: {{module}}.{{objname}}
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:add-heading: Example using ``{{objname}}``:

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