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kMutagenekMutagene
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port project from core
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‎BioFSharp.XYZ.sln renamed to ‎BioFSharp.Interactive.sln

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@@ -5,11 +5,11 @@ VisualStudioVersion = 17.0.31903.59
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{7501C4DF-A844-40A0-8742-3343E48E55F1}"
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EndProject
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.XYZ", "src\BioFSharp.XYZ\BioFSharp.XYZ.fsproj", "{BAC97B5C-B9A6-40D6-B533-0A07E12939ED}"
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.Interactive", "src\BioFSharp.Interactive\BioFSharp.Interactive.fsproj", "{BAC97B5C-B9A6-40D6-B533-0A07E12939ED}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{D152DA0B-8F60-4611-B613-642379E2B17C}"
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EndProject
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.XYZ.Tests", "tests\BioFSharp.XYZ.Tests\BioFSharp.XYZ.Tests.fsproj", "{CB9E38BC-EE86-44EB-AFF5-91D1AF713ADC}"
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.Interactive.Tests", "tests\BioFSharp.Interactive.Tests\BioFSharp.Interactive.Tests.fsproj", "{CB9E38BC-EE86-44EB-AFF5-91D1AF713ADC}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{77A50576-9359-44E5-B2F9-95318AB3DAEA}"
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ProjectSection(SolutionItems) = preProject

‎README.md

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# BioFSharp.XYZ
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# BioFSharp.Interactive
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![Logo](docs/img/Logo_large.png)
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A template repository for creating an extension package for BioFSharp.
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## Content
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- `src/BioFSharp.XYZ`: The main project folder. Contains a library with BioFSharp core dependency.
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- `tests/BioFSharp.XYZ.Tests`: The test project folder. Contains a XUnit test project
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- `src/BioFSharp.Interactive`: The main project folder. Contains a library with BioFSharp core dependency.
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- `tests/BioFSharp.Interactive.Tests`: The test project folder. Contains a XUnit test project
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- `build/build.fsproj`: A FAKE build project that handles building, testing, packaging, publishing, etc.
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- `docs`: the docs folder contains an example index.fsx file with simple documentation boilerplate.
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- Rename some things: Replace `XYZ` with the name of your package
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- `PackageTemplate.sln`
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- `src/BioFSharp.XYZ`
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- `src/BioFSharp.XYZ/BioFSharp.XYZ.fsproj`
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- `src/BioFSharp.Interactive`
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- `src/BioFSharp.Interactive/BioFSharp.Interactive.fsproj`
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- Rename and add nuget package metadata
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- `tests/BioFSharp.XYZ`
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- `tests/BioFSharp.XYZ.Tests/BioFSharp.XYZ.Tests.fsproj`
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- Also make sure to fix the project reference to BioFSharp.XYZ when renamed
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- `tests/BioFSharp.Interactive`
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- `tests/BioFSharp.Interactive.Tests/BioFSharp.Interactive.Tests.fsproj`
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- Also make sure to fix the project reference to BioFSharp.Interactive when renamed
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- in `build/ProjectInfo.fs`:
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- Set project name:
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```fsharp
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let project = "BioFSharp.XYZ" // replace with the name of your project
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let project = "BioFSharp.Interactive" // replace with the name of your project
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```
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- Set git owner:
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```fsharp
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```fsharp
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let testProjects =
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[
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"tests/BioFSharp.XYZ.Tests/BioFSharp.XYZ.Tests.fsproj" // replace with the name of your test project
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"tests/BioFSharp.Interactive.Tests/BioFSharp.Interactive.Tests.fsproj" // replace with the name of your test project
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]
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```
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- in `.github/workflows/build-and-test.yml`: change codecov slug

‎build/ProjectInfo.fs

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open Fake.Core
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let project = "BioFSharp.XYZ"
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let project = "BioFSharp.Interactive"
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let testProjects =
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[
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"tests/BioFSharp.XYZ.Tests/BioFSharp.XYZ.Tests.fsproj"
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"tests/BioFSharp.Interactive.Tests/BioFSharp.Interactive.Tests.fsproj"
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]
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let solutionFile = $"{project}.sln"

‎docs/index.fsx

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(**
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# BioFSharp.XYZ
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# BioFSharp.Interactive
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![Logo](./img/Logo_large.png)
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Make sure to load any external references via nuget.
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*)
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#r "nuget: BioFSharp, 2.0.0-preview.3"
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#I @"..\src\BioFSharp.XYZ\bin\Release\netstandard2.0"
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#r "BioFSharp.XYZ.dll"
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#I @"..\src\BioFSharp.Interactive\bin\Release\netstandard2.0"
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#r "BioFSharp.Interactive.dll"
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open BioFSharp.XYZ
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open BioFSharp.Interactive
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let o = BioTalk.helloBio "Kev"
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‎src/BioFSharp.Interactive/BioFSharp.Interactive.fsproj

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<Project Sdk="Microsoft.NET.Sdk">
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<PropertyGroup>
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<TargetFramework>netstandard2.0</TargetFramework>
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<GenerateDocumentationFile>true</GenerateDocumentationFile>
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<IncludeSymbols>true</IncludeSymbols>
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<SymbolPackageFormat>snupkg</SymbolPackageFormat>
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</PropertyGroup>
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<PropertyGroup>
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<Authors>Kevin Schneider, F# open source contributors</Authors>
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<Description>BioFSharp Formatting extensions for .NET Interactive.</Description>
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<Summary>
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BioFSharp Formatting extensions for .NET Interactive.
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</Summary>
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<PackageLicenseExpression>MIT</PackageLicenseExpression>
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<PackageProjectUrl>https://BioFSharp.github.io/BioFSharp.Interactive/</PackageProjectUrl>
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<PackageIcon>icon.png</PackageIcon>
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<PackageTags>bioinformatics F# fsharp statistic biostatistics datascience</PackageTags>
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<RepositoryUrl>https://github.com/BioFSharp/BioFSharp.Interactive</RepositoryUrl>
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<RepositoryType>git</RepositoryType>
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<FsDocsLicenseLink>https://github.com/BioFSharp/BioFSharp.Interactive/blob/main/LICENSE</FsDocsLicenseLink>
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<FsDocsReleaseNotesLink>https://github.com/BioFSharp/BioFSharp.Interactive/blob/main/RELEASE_NOTES.md</FsDocsReleaseNotesLink>
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</PropertyGroup>
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<ItemGroup>
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<Compile Remove="bin\**" />
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<EmbeddedResource Remove="bin\**" />
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<None Remove="bin\**" />
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</ItemGroup>
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<ItemGroup>
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<Compile Include="Formatters.fs" />
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<Compile Include="Extension.fs" />
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</ItemGroup>
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<ItemGroup>
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<None Include="..\..\docs\img\icon.png" Pack="true" PackagePath=""/>
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<PackageReference Include="BioFSharp" Version="2.0.0-preview.3" />
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<PackageReference Include="BioFSharp.IO" Version="2.0.0-preview.3" />
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<PackageReference Include="Microsoft.DotNet.Interactive" Version="1.0.0-beta.24208.1" />
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<PackageReference Include="Microsoft.DotNet.Interactive.Formatting" Version="1.0.0-beta.24208.1" />
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</ItemGroup>
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<ItemGroup>
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<None Include="$(OutputPath)/BioFSharp.Interactive.dll" Pack="true" PackagePath="interactive-extensions/dotnet" />
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</ItemGroup>
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</Project>

‎src/BioFSharp.Interactive/Extension.fs

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namespace BioFSharp.Interactive
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open System
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open System.Threading.Tasks
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open Microsoft.DotNet.Interactive
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open Microsoft.DotNet.Interactive.Formatting
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open BioFSharp
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open BioFSharp.IO
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type FormatterKernelExtension() =
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interface IKernelExtension with
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member _.OnLoadAsync _ =
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Formatters.registerAll()
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Task.CompletedTask

‎src/BioFSharp.Interactive/Formatters.fs

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namespace BioFSharp.Interactive
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module Formatters =
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open System
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open Microsoft.DotNet.Interactive.Formatting
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open BioFSharp
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open BioFSharp.IO
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let formatAminoAcid (item: AminoAcids.AminoAcid) (writer: IO.TextWriter) =
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let pretty = FSIPrinters.prettyPrintBioItem item
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writer.Write(pretty)
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let formatBioCollection (bioCollection: seq<IBioItem>) (writer: IO.TextWriter) =
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let pretty = $"<pre>{FSIPrinters.prettyPrintBioCollection bioCollection}</pre>"
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writer.Write(pretty)
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let registerAll() =
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Formatter.Register<AminoAcids.AminoAcid>(
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formatAminoAcid,
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"text/html"
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)
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Formatter.Register<seq<IBioItem>>(
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formatBioCollection,
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"text/html"
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)

‎src/BioFSharp.XYZ/Library.fs renamed to ‎src/BioFSharp.Interactive/Library.fs

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namespace BioFSharp.XYZ
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namespace BioFSharp.Interactive
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open BioFSharp
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‎src/BioFSharp.Interactive/Repack.ps1

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# Clean up the previously-cached NuGet packages.
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# Lower-case is intentional (that's how nuget stores those packages).
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Remove-Item -Recurse ~\.nuget\packages\biofsharp.interactive* -Force
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Remove-Item -Recurse ~\.nuget\packages\biofsharp* -Force
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# build and pack Plotly.NET.Interactive
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cd ../../
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dotnet restore
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dotnet build
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dotnet pack -c Release -p:PackageVersion=0.0.0-dev -o "./pkg"
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cd src/BioFSharp.Interactive

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