Migration of BioFSharp to updated Project scaffold. Docs are currentl…

…y ommitted.
CSBiology · Aug 13, 2018 · 67bf014 · 67bf014
1 parent 42937a1
commit 67bf014
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Showing 235 changed files with 24,787 additions and 209,235 deletions.
diff --git a/.editorconfig b/.editorconfig
diff --git a/.gitignore b/.gitignore
@@ -20,7 +20,6 @@ build/
 [Bb]in/
 [Oo]bj/
 
-
 # MSTest test Results
 [Tt]est[Rr]esult*/
 [Bb]uild[Ll]og.*
@@ -170,15 +169,6 @@ $RECYCLE.BIN/
 # NuGet Packages Directory
 packages/
 
-# Generated documentation folder
-docs/formatted/
-
-#ignore local docs
-docs/local/
-
-# Temp folder used for publishing docs
-temp/
-
 # Test results produced by build
 TestResults.xml
 
@@ -189,17 +179,8 @@ release.sh
 localpackages/
 paket-files
 *.orig
-docs/content/license.md
-docs/content/release-notes.md
+docsrc/content/license.md
+docsrc/content/release-notes.md
 .fake
-docs/tools/FSharp.Formatting.svclog
-docs/content/data/Output.txt
-docs/content/data/gffExampleWrite.gff
-docs/content/data/testQuery.fastA
-docs/content/data/Chlamy_Cp.fastA.phr
-docs/content/data/Chlamy_Cp.fastA.pin
-docs/content/data/Chlamy_Cp.fastA.psq
-/docs/content/data/FASTAExample3.fasta
-/docs/content/data/sequenceTestWrite1.gb
-/docs/content/data/sequenceTestWrite2.gb
-/docs/content/data/blastTestOutput.csv
+docsrc/tools/FSharp.Formatting.svclog
+docs
diff --git a/.paket/Paket.Restore.targets b/.paket/Paket.Restore.targets
@@ -71,7 +71,7 @@
       <PaketRestoreRequired Condition=" '$(PaketRestoreLockFileHash)' == '$(PaketRestoreCachedHash)' ">false</PaketRestoreRequired>
       <PaketRestoreRequired Condition=" '$(PaketRestoreLockFileHash)' == '' ">true</PaketRestoreRequired>
     </PropertyGroup>
-    
+
     <PropertyGroup Condition="'$(PaketPropsVersion)' != '5.174.2' ">
       <PaketRestoreRequired>true</PaketRestoreRequired>
     </PropertyGroup>
@@ -96,7 +96,7 @@
       <PaketOriginalReferencesFilePath Condition=" !Exists('$(PaketOriginalReferencesFilePath)')">$(MSBuildProjectDirectory)\$(MSBuildProjectName).paket.references</PaketOriginalReferencesFilePath>
       <!-- paket.references -->
       <PaketOriginalReferencesFilePath Condition=" !Exists('$(PaketOriginalReferencesFilePath)')">$(MSBuildProjectDirectory)\paket.references</PaketOriginalReferencesFilePath>
-      
+
       <DoAllResolvedFilesExist>false</DoAllResolvedFilesExist>
       <DoAllResolvedFilesExist Condition="Exists(%(PaketResolvedFilePaths.Identity))">true</DoAllResolvedFilesExist>
       <PaketRestoreRequired>true</PaketRestoreRequired>

diff --git a/.paket/paket.bootstrapper.exe b/.paket/paket.bootstrapper.exe
diff --git a/.paket/paket.exe b/.paket/paket.exe
diff --git a/.paket/paket.targets b/.paket/paket.targets
diff --git a/.travis.yml b/.travis.yml
@@ -1,11 +1,31 @@
 language: csharp
-mono: latest # until https://github.com/dotnet/sdk/issues/335 is solved we don't have the full benefit of mono
-dotnet: 2.1.101
 
-sudo: false  # use the new container-based Travis infrastructure
+sudo: false  # use the new container-based Travis infrastructure 
+
+mono: 5.12.0
+
+dotnet: 2.1.300
+
+install:
+
+  # workaround for missing .net 4.5 targing pack
+
+  - export FrameworkPathOverride=$(dirname $(which mono))/../lib/mono/4.5/
 
 before_install:
   - chmod +x build.sh
-
-script:
- - ./build.sh RunTests
+
+  matrix:
+  include:
+    - os: linux # Ubuntu 14.04
+      dist: trusty
+      sudo: required
+      dotnet : 2.1.300
+    - os: osx # OSX 10.12
+      osx_image: xcode9.1
+      dotnet : 2.1.300
+      dist: trusty
+      sudo: required
+
+script: 
+  - ./build.sh All
diff --git a/BioFSharp.VC.db b/BioFSharp.VC.db
diff --git a/BioFSharp.sln b/BioFSharp.sln
@@ -1,142 +1,107 @@
+
 Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio 15
-VisualStudioVersion = 15.0.26430.16
+VisualStudioVersion = 15.0.27703.2000
 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", "src\BioFSharp\BioFSharp.fsproj", "{4E235DDD-1B59-4A93-ABE9-2FEEF18B09A1}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp", "src\BioFSharp\BioFSharp.fsproj", "{DC20B62F-9F8B-4128-898D-9436B1CE8B8D}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{BF60BC93-E09B-4E5F-9D85-95A519479D54}"
 	ProjectSection(SolutionItems) = preProject
-		build.fsx = build.fsx
 		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
-		docs\tools\formatters.fsx = docs\tools\formatters.fsx
-		docs\tools\generate.fsx = docs\tools\generate.fsx
-		docs\tools\templates\template.cshtml = docs\tools\templates\template.cshtml
+		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
-		docs\content\Alignment.fsx = docs\content\Alignment.fsx
-		docs\content\AminoProperties.fsx = docs\content\AminoProperties.fsx
-		docs\content\BioCollections.fsx = docs\content\BioCollections.fsx
-		docs\content\BioDB.fsx = docs\content\BioDB.fsx
-		docs\content\BioID.fsx = docs\content\BioID.fsx
-		docs\content\BioItem.fsx = docs\content\BioItem.fsx
-		docs\content\BlastWrapper.fsx = docs\content\BlastWrapper.fsx
-		docs\content\Clustal.fsx = docs\content\Clustal.fsx
-		docs\content\ClustalOWrapper.fsx = docs\content\ClustalOWrapper.fsx
-		docs\content\CSV.fsx = docs\content\CSV.fsx
-		docs\content\FastA.fsx = docs\content\FastA.fsx
-		docs\content\FastQ.fsx = docs\content\FastQ.fsx
-		docs\content\Formula.fsx = docs\content\Formula.fsx
-		docs\content\GenBank.fsx = docs\content\GenBank.fsx
-		docs\content\GESA.fsx = docs\content\GESA.fsx
-		docs\content\GFF3.fsx = docs\content\GFF3.fsx
-		docs\content\index.fsx = docs\content\index.fsx
-		docs\content\Introduction.fsx = docs\content\Introduction.fsx
-		docs\content\license.md = docs\content\license.md
-		docs\content\MoleculeFinding.fsx = docs\content\MoleculeFinding.fsx
-		docs\content\MotiveSearch.fsx = docs\content\MotiveSearch.fsx
-		docs\content\Newick.fsx = docs\content\Newick.fsx
-		docs\content\Obo.fsx = docs\content\Obo.fsx
-		docs\content\ParallelAlignment.fsx = docs\content\ParallelAlignment.fsx
-		docs\content\PetideClassification.fsx = docs\content\PetideClassification.fsx
-		docs\content\Readers.fsx = docs\content\Readers.fsx
-		docs\content\release-notes.md = docs\content\release-notes.md
-		docs\content\StringMatching.fsx = docs\content\StringMatching.fsx
-		docs\content\tutorial.fsx = docs\content\tutorial.fsx
-		docs\content\UniProt.fsx = docs\content\UniProt.fsx
-		docs\content\WebLogo.fsx = docs\content\WebLogo.fsx
+		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("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Tests", "tests\BioFSharp.Tests\BioFSharp.Tests.fsproj", "{12CFF99C-5660-42FE-9370-9085A6558F16}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Tests", "tests\BioFSharp.Tests\BioFSharp.Tests.fsproj", "{EC120240-3BD9-4026-BA39-FEBEF5B7D41B}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FSharpAux", "..\FSharpAux\src\FSharpAux\FSharpAux.fsproj", "{0019D7CC-F9F2-40A6-86CF-AEF143165D36}"
-EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FSharpAux.IO", "..\FSharpAux\src\FSharpAux.IO\FSharpAux.IO.fsproj", "{300079C1-69F3-46CE-9F57-C5510B7E925B}"
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "git", "git", "{078A9C52-DDC1-46F4-9235-9E6C89C87AFD}"
+	ProjectSection(SolutionItems) = preProject
+		.gitattributes = .gitattributes
+		.gitignore = .gitignore
+	EndProjectSection
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.BioDB", "src\BioFSharp.BioDB\BioFSharp.BioDB.fsproj", "{C005AF19-B61C-484F-9E3A-28B497B19C17}"
+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
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.IO", "src\BioFSharp.IO\BioFSharp.IO.fsproj", "{BC61517C-9DD1-4847-8512-0B00434216D7}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.BioDB", "src\BioFSharp.BioDB\BioFSharp.BioDB.fsproj", "{36183ED7-462B-45DF-8FD5-6BD45084985B}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Parallel", "src\BioFSharp.Parallel\BioFSharp.Parallel.fsproj", "{A7B90331-E394-414F-8CBA-27B19B187B0E}"
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.IO", "src\BioFSharp.IO\BioFSharp.IO.fsproj", "{4EBA7C43-6726-4AFE-9EF2-3607CA038A62}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Stats", "src\BioFSharp.Stats\BioFSharp.Stats.fsproj", "{5A448A45-8238-467F-B60F-EB1A6BB8DBBC}"
+Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.Parallel", "src\BioFSharp.Parallel\BioFSharp.Parallel.fsproj", "{12A8066D-B779-425C-A2D2-491693EC6B42}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Vis", "src\BioFSharp.Vis\BioFSharp.Vis.fsproj", "{BBF10BBE-BDFA-414E-8154-1B1BB1D043DD}"
+Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.Stats", "src\BioFSharp.Stats\BioFSharp.Stats.fsproj", "{9562FADF-F2E9-4998-BEF7-B252C55F7A38}"
 EndProject
-Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FSharp.Stats", "..\FSharp.Stats\src\FSharp.Stats\FSharp.Stats.fsproj", "{042658EB-E1CC-476C-A794-5631E6E53855}"
+Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.Vis", "src\BioFSharp.Vis\BioFSharp.Vis.fsproj", "{DBD17E56-E3A2-4A19-AEAB-0E758FEBCD84}"
 EndProject
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 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
-		SolutionGuid = {C50F9EB5-7227-4BA5-AF8F-BCA7F7ECD383}
+		SolutionGuid = {DC87DD12-49BB-4661-B8AB-9D08B005A76B}
 	EndGlobalSection
 EndGlobal
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,2 +1,2 @@
-#### 0.0.1 - September 16 2016
+#### 0.0.1 - Thursday, August 9, 2018
 * Initial release
diff --git a/appveyor.yml b/appveyor.yml
@@ -1,29 +1,11 @@
-version: '0.0.1.{build}'
 image: Visual Studio 2017
-# branches:
-#   only:
-#   - master
-skip_tags: true
+
 init:
-  # Good practise, because Windows line endings are different from Unix/Linux ones
-  - cmd: git config --global core.autocrlf true
-install:
-  # Install repo specific stuff here
-before_build:
-  # Display .NET Core version
-  - cmd: dotnet --version
+  - git config --global core.autocrlf input
 build_script:
-  # output will be in bin
   - cmd: build.cmd All
-after_build:
-  # For once the build has completed
+test: off
+version: 0.0.1.{build}
 artifacts:
- - path: 'bin\*.nupkg'
-   name: FSharp.FGL
-   type: NuGetPackage
-clone_depth: 1
-test_script:
-  # done in build step
-on_finish :
-  # any cleanup in here
-deploy: off
+  - path: bin
+    name: bin