added readme, docs template, license, and github workflow

.github/workflows/CI.yml

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+name: CI
+on:
+ pull_request:
+ branches:
+ - master
+ push:
+ branches:
+ - master
+ tags: '*'
+jobs:
+ test:
+ name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ fail-fast: false
+ matrix:
+ version:
+ - '1.6'
+ - '1'
+ - 'nightly'
+ os:
+ - ubuntu-latest
+ - macOS-latest
+ arch:
+ - x64
+ steps:
+ - uses: actions/checkout@v2
+ - uses: julia-actions/setup-julia@v1
+ with:
+ version: ${{ matrix.version }}
+ arch: ${{ matrix.arch }}
+ - uses: actions/cache@v1
+ env:
+ cache-name: cache-artifacts
+ with:
+ path: ~/.julia/artifacts
+ key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+ restore-keys: |
+ ${{ runner.os }}-test-${{ env.cache-name }}-
+ ${{ runner.os }}-test-
+ ${{ runner.os }}-
+ - uses: julia-actions/julia-buildpkg@v1
+ - uses: julia-actions/julia-runtest@v1
+ continue-on-error: ${{ matrix.version == 'nightly' }}
+ - uses: julia-actions/julia-processcoverage@v1
+ - uses: codecov/codecov-action@v1
+ with:
+ file: lcov.info
+ docs:
+ name: Documentation
+ runs-on: macos-latest
+ steps:
+ - uses: actions/checkout@v2
+ - uses: julia-actions/setup-julia@v1
+ with:
+ version: '1.6'
+ arch: x64
+ - run: |
+ julia --project=docs -e '
+ using Pkg
+ Pkg.develop(PackageSpec(path=pwd()))
+ Pkg.instantiate()'
+ - run: |
+ julia --project=docs -e '
+ using Documenter: DocMeta, doctest
+ using MRFingerprintingRecon
+ DocMeta.setdocmeta!(MRFingerprintingRecon, :DocTestSetup, :(using MRFingerprintingRecon); recursive=true)
+ # doctest(MRFingerprintingRecon)'
+ - run: julia --project=docs docs/make.jl
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+ schedule:
+ - cron: 0 0 * * *
+ workflow_dispatch:
+jobs:
+ CompatHelper:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Pkg.add("CompatHelper")
+ run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+ - name: CompatHelper.main()
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+ run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+ issue_comment:
+ types:
+ - created
+ workflow_dispatch:
+jobs:
+ TagBot:
+ if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+ runs-on: ubuntu-latest
+ steps:
+ - uses: JuliaRegistries/TagBot@v1
+ with:
+ token: ${{ secrets.GITHUB_TOKEN }}
+ ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -1,2 +1,7 @@
+*.out
+.vscode/
+docs/build
+docs/src/build*
+docs/Manifest.toml
 /Manifest.toml
-.vscode
+.DS_Store

LICENSE

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+MIT License
+
+Copyright (c) 2021 Jakob Asslaender <jakob.asslaender@nyumc.org> and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# MRFingerprintingRecon.jl
+
+
+| **Documentation** | **Paper** | **Build Status** |
+|:------------------------- |:--------------------------- |:------------------------------------- |
+| [![][docs-img]][docs-url] | [![][paper-img]][paper-url] | [![][gh-actions-img]][gh-actions-url] |
+| | [![][arXiv-img]][arXiv-url] | [![][codecov-img]][codecov-url] |
+
+
+MRFingerprintingRecon.jl is a Julia package that implements--so far--the *low rank inversion* reconstruction described in the paper [Low rank alternating direction method of multipliers reconstruction for MR fingerprinting](https://doi.org/10.1002/mrm.26639). This package is still work in progress and the interface will likely change over time. The ultimate goal of this package is to reproduce the [Matlab code](https://bitbucket.org/asslaender/nyu_mrf_recon) of the ADMM algorithm to Julia.
+
+
+[docs-img]: https://img.shields.io/badge/docs-latest%20release-blue.svg
+[docs-url]: https://JakobAsslaender.github.io/MRFingerprintingRecon.jl/stable
+
+[gh-actions-img]: https://github.com/JakobAsslaender/MRFingerprintingRecon.jl/workflows/CI/badge.svg
+[gh-actions-url]: https://github.com/JakobAsslaender/MRFingerprintingRecon.jl/actions
+
+[codecov-img]: https://codecov.io/gh/JakobAsslaender/MRFingerprintingRecon.jl/branch/master/graph/badge.svg
+[codecov-url]: https://codecov.io/gh/JakobAsslaender/MRFingerprintingRecon.jl
+
+[arXiv-img]: https://img.shields.io/badge/arXiv-2107.11000-blue.svg
+[arXiv-url]: https://arxiv.org/pdf/1608.06974.pdf
+
+[paper-img]: https://img.shields.io/badge/doi-10.1002/mrm.29071-blue.svg
+[paper-url]: https://doi.org/10.1002/mrm.26639

docs/Project.toml

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+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
+IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+MRFingerprintingRecon = "f4798e02-a7e0-47f5-a571-12dd775704d3"
+PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+WebIO = "0f1e0344-ec1d-5b48-a673-e5cf874b6c29"

docs/make.jl

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+using Pkg
+Pkg.activate("docs")
+Pkg.develop(PackageSpec(path=pwd()))
+Pkg.instantiate()
+
+using MRFingerprintingRecon
+using Documenter
+using Literate
+using Plots # to not capture precompilation output
+
+# HTML Plotting Functionality
+struct HTMLPlot
+ p # :: Plots.Plot
+end
+const ROOT_DIR = joinpath(@__DIR__, "build")
+const PLOT_DIR = joinpath(ROOT_DIR, "plots")
+function Base.show(io::IO, ::MIME"text/html", p::HTMLPlot)
+ mkpath(PLOT_DIR)
+ path = joinpath(PLOT_DIR, string(UInt32(floor(rand()*1e9)), ".html"))
+ Plots.savefig(p.p, path)
+ if get(ENV, "CI", "false") == "true" # for prettyurl
+ print(io, "<object type=\"text/html\" data=\"../../$(relpath(path, ROOT_DIR))\" style=\"width:100%;height:425px;\"></object>")
+ else
+ print(io, "<object type=\"text/html\" data=\"../$(relpath(path, ROOT_DIR))\" style=\"width:100%;height:425px;\"></object>")
+ end
+end
+
+# Notebook hack to display inline math correctly
+function notebook_filter(str)
+ re = r"(?<!`)``(?!`)" # Two backquotes not preceded by nor followed by another
+ return replace(str, re => "\$")
+end
+
+# Literate
+OUTPUT = joinpath(@__DIR__, "src/build_literate")
+
+files = [
+ "tutorial.jl",
+]
+
+for file in files
+ file_path = joinpath(@__DIR__, "src/", file)
+ Literate.markdown(file_path, OUTPUT)
+ Literate.notebook(file_path, OUTPUT, preprocess=notebook_filter; execute=false)
+ Literate.script( file_path, OUTPUT)
+end
+
+DocMeta.setdocmeta!(MRFingerprintingRecon, :DocTestSetup, :(using MRFingerprintingRecon); recursive=true)
+
+makedocs(;
+ doctest = false,
+ modules=[MRFingerprintingRecon],
+ authors="Jakob Asslaender <jakob.asslaender@nyumc.org> and contributors",
+ repo="https://github.com/JakobAsslaender/MRFingerprintingRecon.jl/blob/{commit}{path}#{line}",
+ sitename="MRFingerprintingRecon.jl",
+ format=Documenter.HTML(;
+ prettyurls=get(ENV, "CI", "false") == "true",
+ canonical="https://JakobAsslaender.github.io/MRFingerprintingRecon.jl",
+ assets=String[],
+ ),
+ pages=[
+ "Home" => "index.md",
+ "Quick Start Tutorial" => Any[
+ "build_literate/tutorial.md",
+ ],
+ "API" => "api.md",
+ ],
+)
+
+# Set dark theme as default independent of the OS's settings
+run(`sed -i'.old' 's/var darkPreference = false/var darkPreference = true/g' docs/build/assets/themeswap.js`)
+
+deploydocs(;
+ repo="github.com/JakobAsslaender/MRFingerprintingRecon.jl",
+)

docs/src/api.md

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+```@meta
+Author = "Jakob Assländer"
+CurrentModule = MRFingerprintingRecon
+```
+
+# API
+
+In the following, you find the documentation of all exported functions of the [MRFingerprintingRecon.jl](https://github.com/JakobAsslaender/MRFingerprintingRecon.jl) package:
+
+```@index
+```
+
+```@autodocs
+Modules = [MRFingerprintingRecon]
+```

docs/src/index.md

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+```@meta
+CurrentModule = MRFingerprintingRecon
+```
+
+# MRFingerprintingRecon.jl
+
+Documentation for the [MRFingerprintingRecon.jl](https://github.com/JakobAsslaender/MRFingerprintingRecon.jl) package. Stay tuned for the documentation...
+
+
+The documentation of all exported functions can be found in the [API](@ref) Section.

docs/src/tutorial.jl

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+#md # [![](https://mybinder.org/badge_logo.svg)](@__BINDER_ROOT_URL__/build_literate/tutorial.ipynb)
+
+# # Tutorial
+
+# TODO
+
+# For this example, we need the following packages:
+using MRFingerprintingRecon
+using Plots
+plotlyjs(bg = RGBA(31/255,36/255,36/255,1.0), ticks=:native); #hide #!nb
+

test/Project.toml

@@ -0,0 +1,4 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/cmaps.jl

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+using BenchmarkTools
+using MRFingerprintingRecon
+using Test
+
+# TODO
+@test 1 == 1

test/runtests.jl

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+using MRFingerprintingRecon
+using Test
+
+@testset "Greens_Interpolation" begin
+ include("cmaps.jl")
+end