Merge pull request #53 from CSBiology/developer

Update master with changes until 0.1.0 from developer
CSBiology · May 30, 2019 · 7a9bdc3 · 7a9bdc3
2 parents 7804a95 + 11e22ad
commit 7a9bdc3
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Showing 64 changed files with 6,878 additions and 239 deletions.
diff --git a/.paket/Paket.Restore.targets b/.paket/Paket.Restore.targets
@@ -62,6 +62,11 @@
     <!-- see https://github.com/fsharp/fslang-design/blob/master/RFCs/FS-1032-fsharp-in-dotnet-sdk.md -->
     <DisableImplicitFSharpCoreReference>true</DisableImplicitFSharpCoreReference>
     <DisableImplicitSystemValueTupleReference>true</DisableImplicitSystemValueTupleReference>
+
+    <!-- Disable Paket restore under NCrunch build -->
+    <PaketRestoreDisabled Condition="'$(NCrunch)' == '1'">True</PaketRestoreDisabled>
+
+    <PaketIntermediateOutputPath Condition=" '$(PaketIntermediateOutputPath)' == '' ">$(BaseIntermediateOutputPath.TrimEnd('\').TrimEnd('\/'))</PaketIntermediateOutputPath>
   </PropertyGroup>
 
   <Target Name="PaketBootstrapping" Condition="Exists('$(PaketToolsPath)paket.bootstrapper.proj')">
@@ -102,24 +107,28 @@
       <PaketRestoreRequired Condition=" '$(PaketRestoreLockFileHash)' == '' ">true</PaketRestoreRequired>
     </PropertyGroup>
 
-    <PropertyGroup Condition="'$(PaketPropsVersion)' != '5.174.2' ">
+	<!--
+		This value should match the version in the props generated by paket
+		If they differ, this means we need to do a restore in order to ensure correct dependencies
+	-->
+    <PropertyGroup Condition="'$(PaketPropsVersion)' != '5.185.3' ">
       <PaketRestoreRequired>true</PaketRestoreRequired>
     </PropertyGroup>
 
     <!-- Do a global restore if required -->
     <Exec Command='$(PaketBootStrapperCommand)' Condition=" '$(PaketBootstrapperStyle)' == 'classic' AND Exists('$(PaketBootStrapperExePath)') AND !(Exists('$(PaketExePath)'))" ContinueOnError="false" />
-    <Exec Command='$(PaketCommand) restore' Condition=" '$(PaketRestoreRequired)' == 'true' " ContinueOnError="false" />
-
+    <Exec Command='$(PaketCommand) restore' Condition=" '$(PaketRestoreRequired)' == 'true' AND '$(PaketDisableGlobalRestore)' != 'true' " ContinueOnError="false" />
+    
     <!-- Step 2 Detect project specific changes -->
     <ItemGroup>
       <MyTargetFrameworks Condition="'$(TargetFramework)' != '' " Include="$(TargetFramework)"></MyTargetFrameworks>
       <!-- Don't include all frameworks when msbuild explicitly asks for a single one -->
       <MyTargetFrameworks Condition="'$(TargetFrameworks)' != '' AND '$(TargetFramework)' == '' " Include="$(TargetFrameworks)"></MyTargetFrameworks>
-      <PaketResolvedFilePaths Include="@(MyTargetFrameworks -> '$(MSBuildProjectDirectory)\obj\$(MSBuildProjectFile).%(Identity).paket.resolved')"></PaketResolvedFilePaths>
+      <PaketResolvedFilePaths Include="@(MyTargetFrameworks -> '$(PaketIntermediateOutputPath)\$(MSBuildProjectFile).%(Identity).paket.resolved')"></PaketResolvedFilePaths>
     </ItemGroup>
     <Message Importance="low" Text="MyTargetFrameworks=@(MyTargetFrameworks) PaketResolvedFilePaths=@(PaketResolvedFilePaths)" />
     <PropertyGroup>
-      <PaketReferencesCachedFilePath>$(MSBuildProjectDirectory)\obj\$(MSBuildProjectFile).paket.references.cached</PaketReferencesCachedFilePath>
+      <PaketReferencesCachedFilePath>$(PaketIntermediateOutputPath)\$(MSBuildProjectFile).paket.references.cached</PaketReferencesCachedFilePath>
       <!-- MyProject.fsproj.paket.references has the highest precedence -->
       <PaketOriginalReferencesFilePath>$(MSBuildProjectFullPath).paket.references</PaketOriginalReferencesFilePath>
       <!-- MyProject.paket.references -->
@@ -154,8 +163,8 @@
 
     <!-- Step 3 Restore project specific stuff if required -->
     <Message Condition=" '$(PaketRestoreRequired)' == 'true' " Importance="low" Text="Detected a change ('$(PaketRestoreRequiredReason)') in the project file '$(MSBuildProjectFullPath)', calling paket restore" />
-    <Exec Command='$(PaketCommand) restore --project "$(MSBuildProjectFullPath)" --target-framework "$(TargetFrameworks)"' Condition=" '$(PaketRestoreRequired)' == 'true' AND '$(TargetFramework)' == '' " ContinueOnError="false" />
-    <Exec Command='$(PaketCommand) restore --project "$(MSBuildProjectFullPath)" --target-framework "$(TargetFramework)"' Condition=" '$(PaketRestoreRequired)' == 'true' AND '$(TargetFramework)' != '' " ContinueOnError="false" />
+    <Exec Command='$(PaketCommand) restore --project "$(MSBuildProjectFullPath)" --output-path "$(PaketIntermediateOutputPath)" --target-framework "$(TargetFrameworks)"' Condition=" '$(PaketRestoreRequired)' == 'true' AND '$(TargetFramework)' == '' " ContinueOnError="false" />
+    <Exec Command='$(PaketCommand) restore --project "$(MSBuildProjectFullPath)" --output-path "$(PaketIntermediateOutputPath)" --target-framework "$(TargetFramework)"' Condition=" '$(PaketRestoreRequired)' == 'true' AND '$(TargetFramework)' != '' " ContinueOnError="false" />
 
     <!-- This shouldn't actually happen, but just to be sure. -->
     <PropertyGroup>
@@ -183,11 +192,12 @@
         <ExcludeAssets Condition=" '%(PaketReferencesFileLinesInfo.Splits)' == '6' And %(PaketReferencesFileLinesInfo.CopyLocal) == 'false'">runtime</ExcludeAssets>
         <ExcludeAssets Condition=" '%(PaketReferencesFileLinesInfo.Splits)' != '6' And %(PaketReferencesFileLinesInfo.AllPrivateAssets) == 'exclude'">runtime</ExcludeAssets>
         <Publish Condition=" '$(PackAsTool)' == 'true' ">true</Publish>
+        <AllowExplicitVersion>true</AllowExplicitVersion>
       </PackageReference>
     </ItemGroup>
 
     <PropertyGroup>
-      <PaketCliToolFilePath>$(MSBuildProjectDirectory)/obj/$(MSBuildProjectFile).paket.clitools</PaketCliToolFilePath>
+      <PaketCliToolFilePath>$(PaketIntermediateOutputPath)/$(MSBuildProjectFile).paket.clitools</PaketCliToolFilePath>
     </PropertyGroup>
 
     <ReadLinesFromFile File="$(PaketCliToolFilePath)" >
@@ -206,37 +216,39 @@
 
     <!-- Disabled for now until we know what to do with runtime deps - https://github.com/fsprojects/Paket/issues/2964
     <PropertyGroup>
-      <RestoreConfigFile>$(MSBuildProjectDirectory)/obj/$(MSBuildProjectFile).NuGet.Config</RestoreConfigFile>
+      <RestoreConfigFile>$(PaketIntermediateOutputPath)/$(MSBuildProjectFile).NuGet.Config</RestoreConfigFile>
     </PropertyGroup> -->
 
   </Target>
 
-  <Target Name="PaketDisableDirectPack" AfterTargets="_IntermediatePack" BeforeTargets="GenerateNuspec" Condition="('$(IsPackable)' == '' Or '$(IsPackable)' == 'true') And Exists('$(MSBuildProjectDirectory)/obj/$(MSBuildProjectFile).references')" >
+  <Target Name="PaketDisableDirectPack" AfterTargets="_IntermediatePack" BeforeTargets="GenerateNuspec" Condition="('$(IsPackable)' == '' Or '$(IsPackable)' == 'true') And Exists('$(PaketIntermediateOutputPath)/$(MSBuildProjectFile).references')" >
     <PropertyGroup>
       <ContinuePackingAfterGeneratingNuspec>false</ContinuePackingAfterGeneratingNuspec>
       <DetectedMSBuildVersion>$(MSBuildVersion)</DetectedMSBuildVersion>
       <DetectedMSBuildVersion Condition="$(MSBuildVersion) == ''">15.8.0</DetectedMSBuildVersion>
     </PropertyGroup>
   </Target>
 
-  <Target Name="PaketOverrideNuspec" AfterTargets="GenerateNuspec" Condition="('$(IsPackable)' == '' Or '$(IsPackable)' == 'true') And Exists('$(MSBuildProjectDirectory)/obj/$(MSBuildProjectFile).references')" >
+  <Target Name="PaketOverrideNuspec" AfterTargets="GenerateNuspec" Condition="('$(IsPackable)' == '' Or '$(IsPackable)' == 'true') And Exists('$(PaketIntermediateOutputPath)/$(MSBuildProjectFile).references')" >
     <ItemGroup>
-      <_NuspecFilesNewLocation Include="$(BaseIntermediateOutputPath)$(Configuration)\*.nuspec"/>
+      <_NuspecFilesNewLocation Include="$(PaketIntermediateOutputPath)\$(Configuration)\*.nuspec"/>
       <MSBuildMajorVersion Include="$(DetectedMSBuildVersion.Replace(`-`, `.`).Split(`.`)[0])" />
       <MSBuildMinorVersion Include="$(DetectedMSBuildVersion.Replace(`-`, `.`).Split(`.`)[1])" />
     </ItemGroup>
 
     <PropertyGroup>
       <PaketProjectFile>$(MSBuildProjectDirectory)/$(MSBuildProjectFile)</PaketProjectFile>
       <ContinuePackingAfterGeneratingNuspec>true</ContinuePackingAfterGeneratingNuspec>
+      <UseMSBuild16_0_Pack>false</UseMSBuild16_0_Pack>
+      <UseMSBuild16_0_Pack Condition=" '@(MSBuildMajorVersion)' >= '16' ">true</UseMSBuild16_0_Pack>
       <UseMSBuild15_9_Pack>false</UseMSBuild15_9_Pack>
-      <UseMSBuild15_9_Pack Condition=" '@(MSBuildMajorVersion)' > '15' OR ('@(MSBuildMajorVersion)' == '15' AND '@(MSBuildMinorVersion)' > '8') ">true</UseMSBuild15_9_Pack>
+      <UseMSBuild15_9_Pack Condition=" '@(MSBuildMajorVersion)' == '15' AND '@(MSBuildMinorVersion)' > '8' ">true</UseMSBuild15_9_Pack>
       <UseMSBuild15_8_Pack>false</UseMSBuild15_8_Pack>
-      <UseMSBuild15_8_Pack Condition=" '$(NuGetToolVersion)' != '4.0.0' AND (! $(UseMSBuild15_9_Pack)) ">true</UseMSBuild15_8_Pack>
+      <UseMSBuild15_8_Pack Condition=" '$(NuGetToolVersion)' != '4.0.0' AND (! $(UseMSBuild15_9_Pack)) AND (! $(UseMSBuild16_0_Pack)) ">true</UseMSBuild15_8_Pack>
       <UseNuGet4_Pack>false</UseNuGet4_Pack>
-      <UseNuGet4_Pack Condition=" (! $(UseMSBuild15_8_Pack)) AND (! $(UseMSBuild15_9_Pack)) ">true</UseNuGet4_Pack>
-      <AdjustedNuspecOutputPath>$(BaseIntermediateOutputPath)$(Configuration)</AdjustedNuspecOutputPath>
-      <AdjustedNuspecOutputPath Condition="@(_NuspecFilesNewLocation) == ''">$(BaseIntermediateOutputPath)</AdjustedNuspecOutputPath>
+      <UseNuGet4_Pack Condition=" (! $(UseMSBuild15_8_Pack)) AND (! $(UseMSBuild15_9_Pack)) AND (! $(UseMSBuild16_0_Pack)) ">true</UseNuGet4_Pack>
+      <AdjustedNuspecOutputPath>$(PaketIntermediateOutputPath)\$(Configuration)</AdjustedNuspecOutputPath>
+      <AdjustedNuspecOutputPath Condition="@(_NuspecFilesNewLocation) == ''">$(PaketIntermediateOutputPath)</AdjustedNuspecOutputPath>
     </PropertyGroup>
 
     <ItemGroup>
@@ -250,6 +262,53 @@
     </ConvertToAbsolutePath>
 
     <!-- Call Pack -->
+    <PackTask Condition="$(UseMSBuild16_0_Pack)"
+              PackItem="$(PackProjectInputFile)"
+              PackageFiles="@(_PackageFiles)"
+              PackageFilesToExclude="@(_PackageFilesToExclude)"
+              PackageVersion="$(PackageVersion)"
+              PackageId="$(PackageId)"
+              Title="$(Title)"
+              Authors="$(Authors)"
+              Description="$(Description)"
+              Copyright="$(Copyright)"
+              RequireLicenseAcceptance="$(PackageRequireLicenseAcceptance)"
+              LicenseUrl="$(PackageLicenseUrl)"
+              ProjectUrl="$(PackageProjectUrl)"
+              IconUrl="$(PackageIconUrl)"
+              ReleaseNotes="$(PackageReleaseNotes)"
+              Tags="$(PackageTags)"
+              DevelopmentDependency="$(DevelopmentDependency)"
+              BuildOutputInPackage="@(_BuildOutputInPackage)"
+              TargetPathsToSymbols="@(_TargetPathsToSymbols)"
+              SymbolPackageFormat="symbols.nupkg"
+              TargetFrameworks="@(_TargetFrameworks)"
+              AssemblyName="$(AssemblyName)"
+              PackageOutputPath="$(PackageOutputAbsolutePath)"
+              IncludeSymbols="$(IncludeSymbols)"
+              IncludeSource="$(IncludeSource)"
+              PackageTypes="$(PackageType)"
+              IsTool="$(IsTool)"
+              RepositoryUrl="$(RepositoryUrl)"
+              RepositoryType="$(RepositoryType)"
+              SourceFiles="@(_SourceFiles->Distinct())"
+              NoPackageAnalysis="$(NoPackageAnalysis)"
+              MinClientVersion="$(MinClientVersion)"
+              Serviceable="$(Serviceable)"
+              FrameworkAssemblyReferences="@(_FrameworkAssemblyReferences)"
+              ContinuePackingAfterGeneratingNuspec="$(ContinuePackingAfterGeneratingNuspec)"
+              NuspecOutputPath="$(AdjustedNuspecOutputPath)"
+              IncludeBuildOutput="$(IncludeBuildOutput)"
+              BuildOutputFolders="$(BuildOutputTargetFolder)"
+              ContentTargetFolders="$(ContentTargetFolders)"
+              RestoreOutputPath="$(RestoreOutputAbsolutePath)"
+              NuspecFile="$(NuspecFileAbsolutePath)"
+              NuspecBasePath="$(NuspecBasePath)"
+              NuspecProperties="$(NuspecProperties)"
+              PackageLicenseFile="$(PackageLicenseFile)"
+              PackageLicenseExpression="$(PackageLicenseExpression)"
+              PackageLicenseExpressionVersion="$(PackageLicenseExpressionVersion)" />
+
     <PackTask Condition="$(UseMSBuild15_9_Pack)"
               PackItem="$(PackProjectInputFile)"
               PackageFiles="@(_PackageFiles)"

diff --git a/.paket/paket.exe b/.paket/paket.exe
diff --git a/BioFSharp.sln b/BioFSharp.sln
@@ -32,6 +32,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "content", "content", "{8E6D
 		docsrc\content\BioDB.fsx = docsrc\content\BioDB.fsx
 		docsrc\content\BioID.fsx = docsrc\content\BioID.fsx
 		docsrc\content\BioItem.fsx = docsrc\content\BioItem.fsx
+		docsrc\content\BioTools-tmhmm.fsx = docsrc\content\BioTools-tmhmm.fsx
 		docsrc\content\BlastWrapper.fsx = docsrc\content\BlastWrapper.fsx
 		docsrc\content\Clustal.fsx = docsrc\content\Clustal.fsx
 		docsrc\content\ClustalOWrapper.fsx = docsrc\content\ClustalOWrapper.fsx
@@ -94,6 +95,10 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.Vis", "src\BioFSh
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.ImgP", "src\BioFSharp.ImgP\BioFSharp.ImgP.fsproj", "{1EB6FB44-6B1E-4939-BF49-267D163959FF}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.BioTools", "src\BioFSharp.BioTools\BioFSharp.BioTools.fsproj", "{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}"
+EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "BioFSharp.ML", "src\BioFSharp.ML\BioFSharp.ML.fsproj", "{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -148,6 +153,18 @@ Global
 		{1EB6FB44-6B1E-4939-BF49-267D163959FF}.Mono|Any CPU.Build.0 = Mono|Any CPU
 		{1EB6FB44-6B1E-4939-BF49-267D163959FF}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{1EB6FB44-6B1E-4939-BF49-267D163959FF}.Release|Any CPU.Build.0 = Release|Any CPU
+		{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}.Mono|Any CPU.ActiveCfg = Mono|Any CPU
+		{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}.Mono|Any CPU.Build.0 = Mono|Any CPU
+		{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{9E8A5AED-DD3C-4250-A9B2-164B08238F8E}.Release|Any CPU.Build.0 = Release|Any CPU
+		{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}.Mono|Any CPU.ActiveCfg = Mono|Any CPU
+		{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}.Mono|Any CPU.Build.0 = Mono|Any CPU
+		{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{B46C2CB5-8EC2-425B-9B15-D0BAEF30C08F}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,3 +1,81 @@
+#### 0.1.0 - Thursday, May 30, 2019
+Several bugfixes and additions to multiple sub projects:
+
+* **BioFSharp** (core):
+    * Additional functionality:
+      * [GravyScore](https://github.com/CSBiology/BioFSharp/commit/209c3497e3cdb1db56a0675e0f2a76634a6dbe7a) (Grand Average of Hydropathy) as additional amino acid property
+
+* **BioFSharp.IO**:
+    * Additional functionality:
+      * [GAF Parser](https://github.com/CSBiology/BioFSharp/commit/cbba6a41a9b239e26467f32048aaec3335373faf) for GO Annotation file format: [Gene Association File](http://geneontology.org/docs/go-annotation-file-gaf-format-2.0/)
+      * [Uniprot style Fasta header parser](https://github.com/CSBiology/BioFSharp/commit/f2a16aaa2456b0c431f6d50d0f78a12834671e97)
+      * [FastA to GFF3 converter functions](https://github.com/CSBiology/BioFSharp/commit/2cdd3537398040e1508736bd734b22a67a7c46e7)
+      * [GFF3 Pretty Printer](https://github.com/CSBiology/BioFSharp/commit/eaaa59fbd382721e75fbb9c6558b0ba2ff6afb00) 
+
+    * BugFixes:
+      * [Fix OboParser](https://github.com/CSBiology/BioFSharp/commit/0354c9c13e7a4692f2ab61b80ef86ac8f5bd83c3) just taking the last occurence of the alt_id keyword and discards previous ones.
+      * Fix [Fasta](https://github.com/CSBiology/BioFSharp/commit/aff8eff849deb1cca411faf3c640d53f6e410497) and [GFF3](https://github.com/CSBiology/BioFSharp/commit/d0f059ab899c715a37b7f50318292c8a81f18dd9) writers appending to files instead of recreating
+
+* **BioFSharp.BioTools**:
+    * Additional functionality:
+      * [TMHMM biocontainer API wrapper](https://github.com/CSBiology/BioFSharp/commit/f11cb122df29ccaa0809d3c3c951294a1b645e0f) ([TMHMM](http://www.cbs.dtu.dk/services/TMHMM/) 2.0c predicts transmembrane helices in proteins)
+      * [FastP and Hera biocontainer API wrapper](https://github.com/CSBiology/BioFSharp/commit/28b7654d57824bcdfdb8bae16af2f0f706ed60ad)
+      * [IntaRNA biocontainer API wrapper](https://github.com/CSBiology/BioFSharp/commit/a659496179cd754fbea2fe9ef4030544a35eb68b) ([IntaRNA](https://github.com/BackofenLab/IntaRNA) is a tool for prediction of various nucleotide interactions)
+
+    * BugFixes:
+      * Fix Stream entry closed error in [BioContainer.tarOfStream()](https://github.com/CSBiology/BioFSharp/commit/20f8973ea717208627ef5a7ea0b72cbaecb4103c)
+
+* **BioFSharp.ImgP**:
+    * Additional functionality:
+      * [update 3DCWT correlation calculation to loop](https://github.com/CSBiology/BioFSharp/commit/0b4ffe93755d915da64f4231199b0ec54d4d6c4d)
+
+    * Bugfixes:
+      * [fix height adjustment in ricker](https://github.com/CSBiology/BioFSharp/commit/abab82be1ac9fa0c540acfb5f3ccc6bd5143df1f)
+      * [fix Ricker values for discrete time points](https://github.com/CSBiology/BioFSharp/commit/2bb6bb2b67ea43df2d9fe970bd1445e568df53d4)
+
+#### 0.0.16 - Thursday, March 7, 2019
+ * Fix template files for all nuget packages: 
+   * use correct paths for binaries
+   * update project descriptions
+   * use type project to infer dependencies
+
+#### 0.0.15 - Thursday, March 7, 2019
+ * BioFSharp.ML - project introduction:
+   * Usage of Microsoft's CNTK library with a biological focus:
+   * This project comes with working CNTK integration:
+      * necessary dependencies to use CNTK and its unmanaged libraries
+      * CNTK loadscript: an easy way to load all dependencies of CNTK. load the script and use the resolveCNTKDependencies() function.
+   * Built-in deep neural network 'd::ppop' ([publication](https://www.frontiersin.org/articles/10.3389/fpls.2018.01559/full))
+     * predict peptide observability in mass spectrometry
+     * Classification: functions to determine peptide feature vectors as input for dppop
+     * Prediction: functions to predict peptide observability using the feature vectors prepared in Classification.
+     * NonPlant and Plant models as embedded resources: the two models used in the original Web API. Additionally load custom models.
+ * Othert additions:
+   * BioFSharp.BioTools:
+     * Integration of new tools as biocontainer APIs:
+       * Hera
+       * FastP
+       * ClustalO
+       * HMMER (experimental):
+         * hmmbuild
+         * hmmalign
+         * hmmsearch
+         * hmmscan
+         * hmmemit
+         * hmmpress
+         * hmmconvert
+
+#### 0.0.14 - Tuesday, February 12, 2019
+ * Addition of blast biocontainer support for makeblastdb, blastp, blastn with full parameter wrapping
+ * Extension of BioContainer functionality:
+   * Add windows/unix path conversions and subpath matching to MounInfo
+   * Add execReturnAsync (returns stdout of docker container) and execAsync (redirects stdout/stderr of container)
+
+#### 0.0.13 - Friday, February 8, 2019
+* Addition of the BioTools project, which uses docker.dotnet to use docker images and stream their output to fsi
+* Low level wrapping of multiple docker.dotnet functions for F#
+* Basic functionality for using docker images from fsi
+
 #### 0.0.12 - Friday, December 28, 2018
 * Addition of Pretty Printers, SOFT Parser, GEOFTP functions
 * Improvement and refactoring of Modification functionality