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Merge pull request #11 from BioFSharp/developer
Upgrade to BioFSharp 2.0.0 and modernize the build setup
2 parents 35944b9 + 83d898a commit a873206

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‎.config/dotnet-tools.json‎

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"version": 1,
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"isRoot": true,
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"tools": {
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"fake-cli": {
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"version": "5.20.3",
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"fsdocs-tool": {
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"version": "20.0.0",
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"commands": [
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"fake"
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"fsdocs"
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]
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},
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"fsharp.formatting.commandtool": {
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"version": "11.1.0",
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"dotnet-repl": {
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"version": "0.1.216",
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"commands": [
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"fsdocs"
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"dotnet-repl"
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]
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}
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}

‎.github/CONTRIBUTING.md‎

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@@ -89,14 +89,17 @@ Here is a brief overview of our main projects (also available [here](https://git
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### Build process
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Our F# projects use the [ProjectScaffold](https://github.com/fsprojects/ProjectScaffold) layout. To build our projects, you will need [.NET Core SDK](https://dotnet.microsoft.com/download) and an installation of [FAKE5 CLI]().
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The build is driven by a [FAKE](https://fake.build/) build project in `build/`, invoked through the `build.cmd` / `build.sh` wrappers. You need the [.NET SDK](https://dotnet.microsoft.com/download) version pinned in `global.json`.
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All projects have at least the following build targets:
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The most important build targets:
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|Target|Description|Command Line Arguments|
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|Target|Description|Command Line|
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|---|---|---|
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|Build|Builds the binaries and docs|fake build|
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|ReleaseLocal|Uses Build. Afterwards creates a folder structure so you can see the docs with proper style and relative paths in temp/localDocs. Use this to test documentation. | fake build --target releaselocal|
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|BuildSolution (default)|Cleans and builds the solution|`./build.cmd`|
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|RunTests|Builds and runs the test suite|`./build.cmd runtests`|
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|RunTestsWithCodeCov|Runs the tests with AltCover coverage (writes `codeCov.xml`)|`./build.cmd runtestswithcodecov`|
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|BuildDocs|Builds the documentation site into `output/` (run `dotnet tool restore` once first)|`./build.cmd builddocs`|
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|WatchDocs|Serves the docs locally with live reload (run `dotnet tool restore` once first). Use this to test documentation.|`./build.cmd watchdocs`|
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## How can i contribute?
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### Documentation guidelines
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The docs in our repos are built by the [F# Formatting Documentation tools](http://fsprojects.github.io/FSharp.Formatting/) which parse `.fsx` files in the docsrc/content folder to generate html files. Again, no strict rules here, just a few minor guidelines:
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The docs in our repos are built by [fsdocs](https://fsprojects.github.io/FSharp.Formatting/) (the `fsdocs-tool` pinned in `.config/dotnet-tools.json`), which turns `.md` and `.fsx` files in the `docs/` folder into the html site and generates the API reference from the compiled assemblies. Again, no strict rules here, just a few minor guidelines:
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* If you add or change functionality to a project, please consider adding/changing the respective documentation script. If you dont have time to do that, please comment it on your pull request.
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* If you add or change functionality to a project, please consider adding/changing the respective documentation page. If you dont have time to do that, please comment it on your pull request.
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* Most documentation is written in a tutorial-style manner. If you use external files in your examples, put them into docsrc/content/data.
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* Most documentation is written in a tutorial-style manner. If you use external files in your examples, put them under `docs/`.
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* API References are built from triple frontslash comments (`///`), please consider adding those above the functions/types/classes you are adding.
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‎.github/workflows/build-test.yml‎

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name: Build and test
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on:
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push:
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branches: [ developer, main ]
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pull_request:
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branches: [ developer, main ]
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jobs:
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build-and-test-linux:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Setup .NET
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uses: actions/setup-dotnet@v4
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with:
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dotnet-version: |
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8.x
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10.x
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- name: make script executable
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run: chmod u+x build.sh
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- name: Build and test
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working-directory: ./
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run: ./build.sh runtests
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build-and-test-windows:
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runs-on: windows-latest
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steps:
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- uses: actions/checkout@v4
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- name: Setup .NET
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uses: actions/setup-dotnet@v4
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with:
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dotnet-version: |
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8.x
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10.x
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- name: Build and test
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working-directory: ./
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run: ./build.cmd runtestswithcodecov
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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fail_ci_if_error: false # requires the CODECOV_TOKEN secret to be configured
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files: ./codeCov.xml
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name: codecov-umbrella # optional
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token: ${{ secrets.CODECOV_TOKEN }} # required
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verbose: true # optional (default = false)

‎.github/workflows/deploy-gh-pages.yml‎

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name: Deploy Docs
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on:
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push:
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branches: [ main ]
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paths:
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- 'docs/**'
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permissions:
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contents: write
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: make script executable
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run: chmod u+x build.sh
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- name: Setup .NET
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uses: actions/setup-dotnet@v4
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with:
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dotnet-version: |
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8.x
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10.x
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- name: restore tools
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run: dotnet tool restore
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- name: Build Docs
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working-directory: ./
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run: ./build.sh builddocs
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- name: Deploy
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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folder: output # The folder the action should deploy.

‎.github/workflows/deploy.yml‎

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‎.gitignore‎

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[Dd]ebug/
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[Rr]elease/
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x64/
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build/
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[Bb]in/
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[Oo]bj/
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/codeCov.xml
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/.fsdocs
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/output
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docs/.fsdocs/
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docs/tmp/watch/
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tmp/watch/
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.fsdocs
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/tests/BioFSharp.Mz.Tests/coverage.xml

‎BioFSharp.Mz.sln‎

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# Visual Studio Version 16
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VisualStudioVersion = 16.0.29806.167
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".paket", ".paket", "{63297B98-5CED-492C-A5B7-A5B4F73CF142}"
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ProjectSection(SolutionItems) = preProject
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paket.dependencies = paket.dependencies
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paket.lock = paket.lock
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paket.references = paket.references
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EndProjectSection
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}"
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EndProject
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Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Mz", "src\BioFSharp.Mz\BioFSharp.Mz.fsproj", "{C11E9782-6300-40E5-AE37-32197AD9F78D}"
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EndProject
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Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "build", "build\build.fsproj", "{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{BF60BC93-E09B-4E5F-9D85-95A519479D54}"
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ProjectSection(SolutionItems) = preProject
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README.md = README.md
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RELEASE_NOTES.md = RELEASE_NOTES.md
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EndProjectSection
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tools", "tools", "{83F16175-43B1-4C90-A1EE-8E351C33435D}"
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ProjectSection(SolutionItems) = preProject
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docsrc\files\styles\CSBStyles.css = docsrc\files\styles\CSBStyles.css
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docsrc\tools\generate.fsx = docsrc\tools\generate.fsx
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docsrc\tools\templates\template.cshtml = docsrc\tools\templates\template.cshtml
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EndProjectSection
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "content", "content", "{8E6D5255-776D-4B61-85F9-73C37AA1FB9A}"
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ProjectSection(SolutionItems) = preProject
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docsrc\content\index.fsx = docsrc\content\index.fsx
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docsrc\content\tutorial.fsx = docsrc\content\tutorial.fsx
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EndProjectSection
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{ED8079DD-2B06-4030-9F0F-DC548F98E1C4}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "git", "git", "{078A9C52-DDC1-46F4-9235-9E6C89C87AFD}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".build", ".build", "{7C6D08E7-3EAC-4335-8F4B-252C193C27C9}"
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ProjectSection(SolutionItems) = preProject
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.travis.yml = .travis.yml
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appveyor.yml = appveyor.yml
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build.cmd = build.cmd
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build.fsx = build.fsx
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build.proj = build.proj
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build.sh = build.sh
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EndProjectSection
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EndProject
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{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70}.Release|Any CPU.Build.0 = Release|Any CPU
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{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Release|Any CPU.Build.0 = Release|Any CPU
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EndGlobalSection
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GlobalSection(SolutionProperties) = preSolution
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HideSolutionNode = FALSE
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EndGlobalSection
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GlobalSection(NestedProjects) = preSolution
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{83F16175-43B1-4C90-A1EE-8E351C33435D} = {A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}
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{8E6D5255-776D-4B61-85F9-73C37AA1FB9A} = {A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}
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{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70} = {ED8079DD-2B06-4030-9F0F-DC548F98E1C4}
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EndGlobalSection
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GlobalSection(ExtensibilityGlobals) = postSolution

‎RELEASE_NOTES.md‎

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#### 0.2.0 (Released 2026-08-29)
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* Upgrade to BioFSharp 2.0.0 (bundles the former BioFSharp.IO package) and migrate the codebase over the breaking API changes
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* Align the dependency stack: FSharpAux / FSharpAux.IO 2.1.0, FSharp.Stats 0.6.0, Newtonsoft.Json 13.0.4, Plotly.NET 6.0.0-preview.2
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* Replace the legacy FAKE 5 build script with the FAKE 6 build project ported from BioFSharp (build.cmd / build.sh wrappers, GitHub Actions build-test and gh-pages docs deployment, fsdocs 20 documentation pipeline)
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#### 0.1.5 - Friday, February 19, 2021
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* SignalDetection: add option for peak summation and intensity weighted based mz refinement
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‎appveyor.yml‎

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‎build.cmd‎

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dotnet tool restore
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dotnet fake build %*
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@echo off
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cls
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dotnet run --project ./build/build.fsproj %*

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