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refactor(IO): drop redundant type aliases from entity modules
The post-rename C# types (BioFSharp.FileFormats.INSDC.BioProject etc.) already carry the right names, so the F# `type BioProject = ...BioProject` aliases inside each IO module were a leftover from before the cleanup pass. Remove them: each module now opens BioFSharp.FileFormats.INSDC at the namespace top and references the C# class directly. Callers continue to use BioFSharp.IO.INSDC.BioProject.read etc., and BioFSharp.FileFormats.INSDC.BioProject for the type. Tests.fs simplified the same way — opens both namespaces and constructs each entity by its bare type name. The first smoke test (which asserted typeof<alias> == typeof<C# class>) is dropped since it's now tautological. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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‎src/BioFSharp.IO.INSDC/Analysis.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC Analysis records.
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module Analysis =
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/// An INSDC Analysis record. Alias for `BioFSharp.FileFormats.INSDC.Analysis`.
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type Analysis = BioFSharp.FileFormats.INSDC.Analysis
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/// Read an INSDC Analysis XML record from the file at `filePath`.
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let read (filePath: string) : Analysis =
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XmlSerializer.read<Analysis> filePath

‎src/BioFSharp.IO.INSDC/BioProject.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC BioProject records (called `Project` in the SRA/ENA
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/// XML schema; `BioProject` is the cross-archive INSDC name used throughout
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/// this library).
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module BioProject =
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/// An INSDC BioProject record. Alias for `BioFSharp.FileFormats.INSDC.BioProject`.
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type BioProject = BioFSharp.FileFormats.INSDC.BioProject
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/// Read an INSDC BioProject XML record from the file at `filePath`.
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let read (filePath: string) : BioProject =
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XmlSerializer.read<BioProject> filePath

‎src/BioFSharp.IO.INSDC/BioSample.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC BioSample records (called `Sample` in the SRA/ENA
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/// XML schema; `BioSample` is the cross-archive INSDC name used throughout
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/// this library).
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module BioSample =
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/// An INSDC BioSample record. Alias for `BioFSharp.FileFormats.INSDC.BioSample`.
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type BioSample = BioFSharp.FileFormats.INSDC.BioSample
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/// Read an INSDC BioSample XML record from the file at `filePath`.
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let read (filePath: string) : BioSample =
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XmlSerializer.read<BioSample> filePath

‎src/BioFSharp.IO.INSDC/Experiment.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC Experiment records.
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module Experiment =
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/// An INSDC Experiment record. Alias for `BioFSharp.FileFormats.INSDC.Experiment`.
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type Experiment = BioFSharp.FileFormats.INSDC.Experiment
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/// Read an INSDC Experiment XML record from the file at `filePath`.
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let read (filePath: string) : Experiment =
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XmlSerializer.read<Experiment> filePath

‎src/BioFSharp.IO.INSDC/Receipt.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC Receipt records (the response document returned by the
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/// ENA submission API).
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module Receipt =
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/// An INSDC Receipt record. Alias for `BioFSharp.FileFormats.INSDC.Receipt`.
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type Receipt = BioFSharp.FileFormats.INSDC.Receipt
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/// Read an INSDC Receipt XML record from the file at `filePath`.
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let read (filePath: string) : Receipt =
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XmlSerializer.read<Receipt> filePath

‎src/BioFSharp.IO.INSDC/Run.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC Run records.
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module Run =
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/// An INSDC Run record. Alias for `BioFSharp.FileFormats.INSDC.Run`.
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type Run = BioFSharp.FileFormats.INSDC.Run
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/// Read an INSDC Run XML record from the file at `filePath`.
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let read (filePath: string) : Run =
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XmlSerializer.read<Run> filePath

‎src/BioFSharp.IO.INSDC/Study.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC Study records.
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module Study =
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/// An INSDC Study record. Alias for `BioFSharp.FileFormats.INSDC.Study`.
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type Study = BioFSharp.FileFormats.INSDC.Study
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/// Read an INSDC Study XML record from the file at `filePath`.
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let read (filePath: string) : Study =
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XmlSerializer.read<Study> filePath

‎src/BioFSharp.IO.INSDC/Submission.fs‎

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namespace BioFSharp.IO.INSDC
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC.Internal
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/// Read and write INSDC Submission records.
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module Submission =
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/// An INSDC Submission record. Alias for `BioFSharp.FileFormats.INSDC.Submission`.
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type Submission = BioFSharp.FileFormats.INSDC.Submission
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/// Read an INSDC Submission XML record from the file at `filePath`.
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let read (filePath: string) : Submission =
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XmlSerializer.read<Submission> filePath

‎tests/BioFSharp.INSDC.Tests/Tests.fs‎

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open Xunit
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open BioFSharp.FileFormats.INSDC
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open BioFSharp.IO.INSDC
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/// Smoke tests that the IO surface compiles and the type aliases line up.
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/// Real fixture-based read/roundtrip tests land in step 4 of plans/implementation.md.
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/// Smoke tests that the IO surface compiles and `writeString` runs for every
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/// entity. Real fixture-based read/roundtrip tests land in step 4 of
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/// plans/implementation.md.
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type IoSurfaceSmokeTests() =
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[<Fact>]
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let ``BioProject.BioProject aliases the generated INSDC BioProject type`` () =
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Assert.Equal(typeof<BioProject.BioProject>, typeof<BioFSharp.FileFormats.INSDC.BioProject>)
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[<Fact>]
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let ``Every entity module exposes a writeString function over its type alias`` () =
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let ``Every entity module's writeString runs on a default-initialised value`` () =
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// Constructing a default-initialised record and round-tripping it through
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// writeString is the cheapest sanity check that XmlSerializer can handle each entity.
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let project = BioProject.BioProject()
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let study = Study.Study()
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let sample = BioSample.BioSample()
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let experiment = Experiment.Experiment()
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let run = Run.Run()
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let analysis = Analysis.Analysis()
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let submission = Submission.Submission()
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let receipt = Receipt.Receipt()
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// None of these should throw; we don't assert on the XML body shape here.
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BioProject.writeString project |> ignore
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Study.writeString study |> ignore
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BioSample.writeString sample |> ignore
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Experiment.writeString experiment |> ignore
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Run.writeString run |> ignore
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Analysis.writeString analysis |> ignore
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Submission.writeString submission |> ignore
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Receipt.writeString receipt |> ignore
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// writeString is the cheapest sanity check that XmlSerializer can handle
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// each entity. We don't assert on the XML body shape here.
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BioProject.writeString (BioProject()) |> ignore
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Study.writeString (Study()) |> ignore
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BioSample.writeString (BioSample()) |> ignore
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Experiment.writeString (Experiment()) |> ignore
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Run.writeString (Run()) |> ignore
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Analysis.writeString (Analysis()) |> ignore
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Submission.writeString (Submission()) |> ignore
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Receipt.writeString (Receipt()) |> ignore

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