From a9ac4531f37ae466a5a5585817624abe37f9a8f3 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 14:08:24 +0200 Subject: [PATCH 01/10] Move CI file to .github/workflows --- build-and-test.yml => .github/workflows/build-and-test.yml | 0 Ontology.NET.sln | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename build-and-test.yml => .github/workflows/build-and-test.yml (100%) diff --git a/build-and-test.yml b/.github/workflows/build-and-test.yml similarity index 100% rename from build-and-test.yml rename to .github/workflows/build-and-test.yml diff --git a/Ontology.NET.sln b/Ontology.NET.sln index 956b2cb..47c8c5c 100644 --- a/Ontology.NET.sln +++ b/Ontology.NET.sln @@ -25,7 +25,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{CE3D EndProject Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".ci", ".ci", "{F9AB2DC2-AB20-4AC2-A827-82819C82D4FA}" ProjectSection(SolutionItems) = preProject - build-and-test.yml = build-and-test.yml + .github\workflows\build-and-test.yml = .github\workflows\build-and-test.yml EndProjectSection EndProject Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "ControlledVocabulary", "src\ControlledVocabulary\ControlledVocabulary.fsproj", "{27679102-2E6D-4BD9-9DF4-FC101EA6487D}" From c670f264e231e4c04e3f945095495565c56c98f9 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 14:29:15 +0200 Subject: [PATCH 02/10] Try fix for build & test CI --- .github/workflows/build-and-test.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index f19839c..ba535e7 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -18,12 +18,16 @@ jobs: uses: actions/setup-dotnet@v3 with: dotnet-version: 8.x.x + + - name: Clear NuGet cache + run: dotnet nuget locals all --clear + - 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 From a181df72a7d67a1f807faf897ce372a0552bc018 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 14:31:48 +0200 Subject: [PATCH 03/10] Add diagnostic steps to CI build & test file --- .github/workflows/build-and-test.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index ba535e7..ec3ffa3 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -19,9 +19,15 @@ jobs: with: dotnet-version: 8.x.x - - name: Clear NuGet cache + - name: Print NuGet sources, before clear + run: dotnet nuget list source + + - name: Clear NuGet cache # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. run: dotnet nuget locals all --clear + - name: Print NuGet sources, after clear + run: dotnet nuget list source + - name: make script executable run: chmod u+x build.sh - name: Build and test From b5a988739abd1f1082fdcde68953ace7aa22b643 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 14:54:28 +0200 Subject: [PATCH 04/10] Try fix build & test CI --- .github/workflows/build-and-test.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index ec3ffa3..fad25bf 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -19,14 +19,11 @@ jobs: with: dotnet-version: 8.x.x - - name: Print NuGet sources, before clear - run: dotnet nuget list source - - name: Clear NuGet cache # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. run: dotnet nuget locals all --clear - - name: Print NuGet sources, after clear - run: dotnet nuget list source + - name: Restore dependencies + run: dotnet restore --force-evaluate - name: make script executable run: chmod u+x build.sh From 77e93d09f97e105ff387265f2e8b442593892510 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 15:04:14 +0200 Subject: [PATCH 05/10] Apply CI fix to Windows part --- .github/workflows/build-and-test.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index fad25bf..9894c28 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -41,6 +41,13 @@ jobs: uses: actions/setup-dotnet@v3 with: dotnet-version: 8.x.x + + - name: Clear NuGet cache # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. + run: dotnet nuget locals all --clear + + - name: Restore dependencies + run: dotnet restore --force-evaluate + - name: Build and test working-directory: ./ run: ./build.cmd runtests From 1ba7d6f9f53dea1747e1e69e305fa2fa6fa78bd3 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 15:05:56 +0200 Subject: [PATCH 06/10] Delete useless cache clearing --- .github/workflows/build-and-test.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index 9894c28..8fea219 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -19,14 +19,13 @@ jobs: with: dotnet-version: 8.x.x - - name: Clear NuGet cache # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. - run: dotnet nuget locals all --clear - + # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. - name: Restore dependencies run: dotnet restore --force-evaluate - name: make script executable run: chmod u+x build.sh + - name: Build and test run: ./build.sh runtests @@ -42,9 +41,7 @@ jobs: with: dotnet-version: 8.x.x - - name: Clear NuGet cache # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. - run: dotnet nuget locals all --clear - + # to prevent error NU1403: Package content hash validation failed for FSharp.Core.8.0.403. The package is different than the last restore. - name: Restore dependencies run: dotnet restore --force-evaluate From 8a3d0ba2ba8fd4a3865e3b32a792cc31ff401733 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 15:17:22 +0200 Subject: [PATCH 07/10] Add diagnostic print line to fix unix CI error --- src/Ontology.NET/OBO/OboOntology.fs | 1 + 1 file changed, 1 insertion(+) diff --git a/src/Ontology.NET/OBO/OboOntology.fs b/src/Ontology.NET/OBO/OboOntology.fs index 8381886..f9dfaaa 100644 --- a/src/Ontology.NET/OBO/OboOntology.fs +++ b/src/Ontology.NET/OBO/OboOntology.fs @@ -258,6 +258,7 @@ type OboOntology = if Option.isSome basePath then let basePathDir = (Option.get >> getOrReturnDir) basePath let totalFilePath = Path.Combine(basePathDir, trimSlashes rfp) + printfn $"fullpath from relpath: {totalFilePath}" totalFilePath else raise (System.ArgumentException($"basePath is None but must be provided when relative path is given.")) From 5e2ad1fd059614a8b504b1a4e7ecde64b24f79a7 Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 15:23:17 +0200 Subject: [PATCH 08/10] Revert "Add diagnostic print line to fix unix CI error" This reverts commit 8a3d0ba2ba8fd4a3865e3b32a792cc31ff401733. --- src/Ontology.NET/OBO/OboOntology.fs | 1 - 1 file changed, 1 deletion(-) diff --git a/src/Ontology.NET/OBO/OboOntology.fs b/src/Ontology.NET/OBO/OboOntology.fs index f9dfaaa..8381886 100644 --- a/src/Ontology.NET/OBO/OboOntology.fs +++ b/src/Ontology.NET/OBO/OboOntology.fs @@ -258,7 +258,6 @@ type OboOntology = if Option.isSome basePath then let basePathDir = (Option.get >> getOrReturnDir) basePath let totalFilePath = Path.Combine(basePathDir, trimSlashes rfp) - printfn $"fullpath from relpath: {totalFilePath}" totalFilePath else raise (System.ArgumentException($"basePath is None but must be provided when relative path is given.")) From 2a81bf4cb40a376757d240c5f2d2fa3feb4609ea Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 15:23:55 +0200 Subject: [PATCH 09/10] Correct folder name in project file display --- tests/Ontology.NET.Tests/Ontology.NET.Tests.fsproj | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/Ontology.NET.Tests/Ontology.NET.Tests.fsproj b/tests/Ontology.NET.Tests/Ontology.NET.Tests.fsproj index 0b1b24f..e16ac71 100644 --- a/tests/Ontology.NET.Tests/Ontology.NET.Tests.fsproj +++ b/tests/Ontology.NET.Tests/Ontology.NET.Tests.fsproj @@ -21,10 +21,10 @@ - - - - + + + + From 3ef7023702c4e0721d64459f9b479587e654911f Mon Sep 17 00:00:00 2001 From: Oliver Maus Date: Thu, 31 Jul 2025 15:24:19 +0200 Subject: [PATCH 10/10] Correct folder path to match Unix's case sensitivity --- tests/Ontology.NET.Tests/OBO/OboOntology.Tests.fs | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/Ontology.NET.Tests/OBO/OboOntology.Tests.fs b/tests/Ontology.NET.Tests/OBO/OboOntology.Tests.fs index a37fd55..a4ce412 100644 --- a/tests/Ontology.NET.Tests/OBO/OboOntology.Tests.fs +++ b/tests/Ontology.NET.Tests/OBO/OboOntology.Tests.fs @@ -59,9 +59,9 @@ module OboOntologyTests = let testFile1 = try OboOntology.fromFile false testFile1Path |> Some with _ -> None let testFile2 = try OboOntology.fromFile false testFile2Path |> Some with _ -> None let testFile3 = try OboOntology.fromFile false testFile3Path |> Some with _ -> None - let testOboFile3Path = Path.Combine(__SOURCE_DIRECTORY__, "references", "testOboFile3.obo") + let testOboFile3Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "testOboFile3.obo") let testOboFile3 = try OboOntology.fromFile false testOboFile3Path |> Some with _ -> None - let goPath = Path.Combine(__SOURCE_DIRECTORY__, "references", "go.obo") + let goPath = Path.Combine(__SOURCE_DIRECTORY__, "References", "go.obo") let go = try OboOntology.fromFile false goPath |> Some with _ -> None