BioFSharp · caroott · Aug 30, 2026 · Aug 29, 2026 · Aug 29, 2026 · Aug 29, 2026
diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json
@@ -2,16 +2,16 @@
   "version": 1,
   "isRoot": true,
   "tools": {
-    "fake-cli": {
-      "version": "5.20.3",
+    "fsdocs-tool": {
+      "version": "20.0.0",
       "commands": [
-        "fake"
+        "fsdocs"
       ]
     },
-    "fsharp.formatting.commandtool": {
-      "version": "11.1.0",
+    "dotnet-repl": {
+      "version": "0.1.216",
       "commands": [
-        "fsdocs"
+        "dotnet-repl"
       ]
     }
   }

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -89,14 +89,17 @@ Here is a brief overview of our main projects (also available [here](https://git
 
 ### Build process
 
-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]().
+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`.
 
-All projects have at least the following build targets:
+The most important build targets:
 
-|Target|Description|Command Line Arguments|
+|Target|Description|Command Line|
 |---|---|---|
-|Build|Builds the binaries and docs|fake build|
-|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|
+|BuildSolution (default)|Cleans and builds the solution|`./build.cmd`|
+|RunTests|Builds and runs the test suite|`./build.cmd runtests`|
+|RunTestsWithCodeCov|Runs the tests with AltCover coverage (writes `codeCov.xml`)|`./build.cmd runtestswithcodecov`|
+|BuildDocs|Builds the documentation site into `output/` (run `dotnet tool restore` once first)|`./build.cmd builddocs`|
+|WatchDocs|Serves the docs locally with live reload (run `dotnet tool restore` once first). Use this to test documentation.|`./build.cmd watchdocs`|
 
 ## How can i contribute?
 
@@ -196,11 +199,11 @@ One of our biggest weakness at the moment are unit tests. We will love everyone
 
 ### Documentation guidelines
 
-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:
+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:
 
-* 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.
+* 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.
 
-* Most documentation is written in a tutorial-style manner. If you use external files in your examples, put them into docsrc/content/data.
+* Most documentation is written in a tutorial-style manner. If you use external files in your examples, put them under `docs/`.
 
 * API References are built from triple frontslash comments (`///`), please consider adding those above the functions/types/classes you are adding.
 

diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -0,0 +1,50 @@
+name: Build and test
+
+on:
+  push:
+    branches: [ developer, main ]
+  pull_request:
+    branches: [ developer, main ]
+
+jobs:
+  build-and-test-linux:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: |
+          8.x
+          10.x
+    - name: make script executable
+      run: chmod u+x build.sh
+    - name: Build and test
+      working-directory: ./
+      run: ./build.sh runtests
+
+  build-and-test-windows:
+
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: |
+          8.x
+          10.x
+    - name: Build and test
+      working-directory: ./
+      run: ./build.cmd runtestswithcodecov
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        fail_ci_if_error: false # requires the CODECOV_TOKEN secret to be configured
+        files: ./codeCov.xml
+        name: codecov-umbrella # optional
+        token: ${{ secrets.CODECOV_TOKEN }} # required
+        verbose: true # optional (default = false)
diff --git a/.github/workflows/deploy-gh-pages.yml b/.github/workflows/deploy-gh-pages.yml
@@ -0,0 +1,34 @@
+name: Deploy Docs
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - 'docs/**'
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: make script executable
+        run: chmod u+x build.sh
+      - name: Setup .NET
+        uses: actions/setup-dotnet@v4
+        with:
+          dotnet-version: |
+            8.x
+            10.x
+      - name: restore tools
+        run: dotnet tool restore
+      - name: Build Docs
+        working-directory: ./
+        run: ./build.sh builddocs
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: output # The folder the action should deploy.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
diff --git a/.gitignore b/.gitignore
@@ -16,7 +16,6 @@
 [Dd]ebug/
 [Rr]elease/
 x64/
-build/
 [Bb]in/
 [Oo]bj/
 
@@ -185,3 +184,8 @@ temp
 /codeCov.xml
 /.fsdocs
 /output
+docs/.fsdocs/
+docs/tmp/watch/
+tmp/watch/
+.fsdocs
+/tests/BioFSharp.Mz.Tests/coverage.xml
diff --git a/BioFSharp.Mz.sln b/BioFSharp.Mz.sln
@@ -2,36 +2,16 @@
 # Visual Studio Version 16
 VisualStudioVersion = 16.0.29806.167
 MinimumVisualStudioVersion = 10.0.40219.1
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".paket", ".paket", "{63297B98-5CED-492C-A5B7-A5B4F73CF142}"
-	ProjectSection(SolutionItems) = preProject
-		paket.dependencies = paket.dependencies
-		paket.lock = paket.lock
-		paket.references = paket.references
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}"
-EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Mz", "src\BioFSharp.Mz\BioFSharp.Mz.fsproj", "{C11E9782-6300-40E5-AE37-32197AD9F78D}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "build", "build\build.fsproj", "{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}"
+EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{BF60BC93-E09B-4E5F-9D85-95A519479D54}"
 	ProjectSection(SolutionItems) = preProject
 		README.md = README.md
 		RELEASE_NOTES.md = RELEASE_NOTES.md
 	EndProjectSection
 EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tools", "tools", "{83F16175-43B1-4C90-A1EE-8E351C33435D}"
-	ProjectSection(SolutionItems) = preProject
-		docsrc\files\styles\CSBStyles.css = docsrc\files\styles\CSBStyles.css
-		docsrc\tools\generate.fsx = docsrc\tools\generate.fsx
-		docsrc\tools\templates\template.cshtml = docsrc\tools\templates\template.cshtml
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "content", "content", "{8E6D5255-776D-4B61-85F9-73C37AA1FB9A}"
-	ProjectSection(SolutionItems) = preProject
-		docsrc\content\index.fsx = docsrc\content\index.fsx
-		docsrc\content\tutorial.fsx = docsrc\content\tutorial.fsx
-	EndProjectSection
-EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{ED8079DD-2B06-4030-9F0F-DC548F98E1C4}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "git", "git", "{078A9C52-DDC1-46F4-9235-9E6C89C87AFD}"
@@ -48,11 +28,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "git", "git", "{078A9C52-DDC
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".build", ".build", "{7C6D08E7-3EAC-4335-8F4B-252C193C27C9}"
 	ProjectSection(SolutionItems) = preProject
-		.travis.yml = .travis.yml
-		appveyor.yml = appveyor.yml
 		build.cmd = build.cmd
-		build.fsx = build.fsx
-		build.proj = build.proj
 		build.sh = build.sh
 	EndProjectSection
 EndProject
@@ -78,13 +54,15 @@ Global
 		{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70}.Release|Any CPU.Build.0 = Release|Any CPU
+		{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{A3C577D1-8E42-4A6B-9F30-6C5D21B0E7A4}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
 	GlobalSection(NestedProjects) = preSolution
-		{83F16175-43B1-4C90-A1EE-8E351C33435D} = {A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}
-		{8E6D5255-776D-4B61-85F9-73C37AA1FB9A} = {A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}
 		{D83DA3EA-3EBB-42EF-99AB-2E0DDC5A5E70} = {ED8079DD-2B06-4030-9F0F-DC548F98E1C4}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,3 +1,9 @@
+#### 0.2.0 (Released 2026-08-29)
+
+* Upgrade to BioFSharp 2.0.0 (bundles the former BioFSharp.IO package) and migrate the codebase over the breaking API changes
+* 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
+* 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)
+
 #### 0.1.5 - Friday, February 19, 2021
 * SignalDetection: add option for peak summation and intensity weighted based mz refinement
 

diff --git a/appveyor.yml b/appveyor.yml
diff --git a/build.cmd b/build.cmd
@@ -1,2 +1,4 @@
-dotnet tool restore
-dotnet fake build %*
+@echo off
+cls
+
+dotnet run --project ./build/build.fsproj %*