small fixes in python and setup instructions

nfdi4plants · Mar 1, 2024 · 9385d06 · 9385d06
1 parent 66b83a2
commit 9385d06
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diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ and __JavaScript__! ❤️
 ``` 
 
 ```bash
-<PackageReference Include="ARCtrl" Version="1.0.0-beta.1" />
+<PackageReference Include="ARCtrl" Version="1.1.0" />
 ```
 
 ### JavaScript
@@ -44,10 +44,27 @@ Currently we provide some documentation in form of markdown files in the `/docs`
     - verify with `npm --version` (Tested with v9.2.0)
 - [.NET SDK](https://dotnet.microsoft.com/en-us/download)
     - verify with `dotnet --version` (Tested with 7.0.306)
+- [Python](https://www.python.org/downloads/)
+    - verify with `py --version` (Tested with 3.12.2)
 
 ### Local Setup
 
-1. `dotnet tool restore`
-3. `npm install`
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+2. Install NPM dependencies
+
+   `npm install`
+
+3. Setup python environment
+
+   `py -m venv .venv`
+
+4. Install [Poetry](https://python-poetry.org/) and dependencies
+
+   1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
+   2. `.\.venv\Scripts\python.exe -m pip install poetry`
+   3. `.\.venv\Scripts\python.exe -m poetry install --no-root`
 
 Verify correct setup with `./build.cmd runtests` ✨
diff --git a/src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj b/src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj
@@ -5,29 +5,29 @@
     <GenerateDocumentationFile>true</GenerateDocumentationFile>
   </PropertyGroup>
   <ItemGroup>
-    <Compile Include="context/ro-crate/isa_assay_context.fs" />
-    <Compile Include="context/ro-crate/isa_comment_context.fs" />
-    <Compile Include="context/ro-crate/isa_component_context.fs" />
-    <Compile Include="context/ro-crate/isa_data_context.fs" />
-    <Compile Include="context/ro-crate/isa_factor_context.fs" />
-    <Compile Include="context/ro-crate/isa_factor_value_context.fs" />
-    <Compile Include="context/ro-crate/isa_investigation_context.fs" />
-    <Compile Include="context/ro-crate/isa_material_attribute_context.fs" />
-    <Compile Include="context/ro-crate/isa_material_attribute_value_context.fs" />
-    <Compile Include="context/ro-crate/isa_material_context.fs" />
-    <Compile Include="context/ro-crate/isa_ontology_annotation_context.fs" />
-    <Compile Include="context/ro-crate/isa_ontology_source_reference_context.fs" />
-    <Compile Include="context/ro-crate/isa_organization_context.fs" />
-    <Compile Include="context/ro-crate/isa_person_context.fs" />
-    <Compile Include="context/ro-crate/isa_process_context.fs" />
-    <Compile Include="context/ro-crate/isa_process_parameter_value_context.fs" />
-    <Compile Include="context/ro-crate/isa_protocol_context.fs" />
-    <Compile Include="context/ro-crate/isa_protocol_parameter_context.fs" />
-    <Compile Include="context/ro-crate/isa_publication_context.fs" />
-    <Compile Include="context/ro-crate/isa_sample_context.fs" />
-    <Compile Include="context/ro-crate/isa_source_context.fs" />
-    <Compile Include="context/ro-crate/isa_study_context.fs" />
-    <Compile Include="context/ro-crate/rocrate_context.fs" />
+    <Compile Include="context\rocrate\isa_assay_context.fs" />
+    <Compile Include="context\rocrate\isa_comment_context.fs" />
+    <Compile Include="context\rocrate\isa_component_context.fs" />
+    <Compile Include="context\rocrate\isa_data_context.fs" />
+    <Compile Include="context\rocrate\isa_factor_context.fs" />
+    <Compile Include="context\rocrate\isa_factor_value_context.fs" />
+    <Compile Include="context\rocrate\isa_investigation_context.fs" />
+    <Compile Include="context\rocrate\isa_material_attribute_context.fs" />
+    <Compile Include="context\rocrate\isa_material_attribute_value_context.fs" />
+    <Compile Include="context\rocrate\isa_material_context.fs" />
+    <Compile Include="context\rocrate\isa_ontology_annotation_context.fs" />
+    <Compile Include="context\rocrate\isa_ontology_source_reference_context.fs" />
+    <Compile Include="context\rocrate\isa_organization_context.fs" />
+    <Compile Include="context\rocrate\isa_person_context.fs" />
+    <Compile Include="context\rocrate\isa_process_context.fs" />
+    <Compile Include="context\rocrate\isa_process_parameter_value_context.fs" />
+    <Compile Include="context\rocrate\isa_protocol_context.fs" />
+    <Compile Include="context\rocrate\isa_protocol_parameter_context.fs" />
+    <Compile Include="context\rocrate\isa_publication_context.fs" />
+    <Compile Include="context\rocrate\isa_sample_context.fs" />
+    <Compile Include="context\rocrate\isa_source_context.fs" />
+    <Compile Include="context\rocrate\isa_study_context.fs" />
+    <Compile Include="context\rocrate\rocrate_context.fs" />
     <Compile Include="ConverterOptions.fs" />
     <Compile Include="Decode.fs" />
     <Compile Include="GEncode.fs" />

diff --git a/...son/context/ro-crate/isa_assay_context.fs → ...Json/context/rocrate/isa_assay_context.fs b/...son/context/ro-crate/isa_assay_context.fs → ...Json/context/rocrate/isa_assay_context.fs
diff --git a/...n/context/ro-crate/isa_comment_context.fs → ...on/context/rocrate/isa_comment_context.fs b/...n/context/ro-crate/isa_comment_context.fs → ...on/context/rocrate/isa_comment_context.fs
diff --git a/...context/ro-crate/isa_component_context.fs → .../context/rocrate/isa_component_context.fs b/...context/ro-crate/isa_component_context.fs → .../context/rocrate/isa_component_context.fs
diff --git a/...Json/context/ro-crate/isa_data_context.fs → ....Json/context/rocrate/isa_data_context.fs b/...Json/context/ro-crate/isa_data_context.fs → ....Json/context/rocrate/isa_data_context.fs
diff --git a/...on/context/ro-crate/isa_factor_context.fs → ...son/context/rocrate/isa_factor_context.fs b/...on/context/ro-crate/isa_factor_context.fs → ...son/context/rocrate/isa_factor_context.fs
diff --git a/...text/ro-crate/isa_factor_value_context.fs → ...ntext/rocrate/isa_factor_value_context.fs b/...text/ro-crate/isa_factor_value_context.fs → ...ntext/rocrate/isa_factor_value_context.fs
diff --git a/...ext/ro-crate/isa_investigation_context.fs → ...text/rocrate/isa_investigation_context.fs b/...ext/ro-crate/isa_investigation_context.fs → ...text/rocrate/isa_investigation_context.fs
diff --git a/...o-crate/isa_material_attribute_context.fs → ...rocrate/isa_material_attribute_context.fs b/...o-crate/isa_material_attribute_context.fs → ...rocrate/isa_material_attribute_context.fs
diff --git a/...e/isa_material_attribute_value_context.fs → ...e/isa_material_attribute_value_context.fs b/...e/isa_material_attribute_value_context.fs → ...e/isa_material_attribute_value_context.fs
diff --git a/.../context/ro-crate/isa_material_context.fs → ...n/context/rocrate/isa_material_context.fs b/.../context/ro-crate/isa_material_context.fs → ...n/context/rocrate/isa_material_context.fs
diff --git a/...-crate/isa_ontology_annotation_context.fs → ...ocrate/isa_ontology_annotation_context.fs b/...-crate/isa_ontology_annotation_context.fs → ...ocrate/isa_ontology_annotation_context.fs
diff --git a/.../isa_ontology_source_reference_context.fs → .../isa_ontology_source_reference_context.fs b/.../isa_ontology_source_reference_context.fs → .../isa_ontology_source_reference_context.fs
diff --git a/...text/ro-crate/isa_organization_context.fs → ...ntext/rocrate/isa_organization_context.fs b/...text/ro-crate/isa_organization_context.fs → ...ntext/rocrate/isa_organization_context.fs
diff --git a/...on/context/ro-crate/isa_person_context.fs → ...son/context/rocrate/isa_person_context.fs b/...on/context/ro-crate/isa_person_context.fs → ...son/context/rocrate/isa_person_context.fs
diff --git a/...n/context/ro-crate/isa_process_context.fs → ...on/context/rocrate/isa_process_context.fs b/...n/context/ro-crate/isa_process_context.fs → ...on/context/rocrate/isa_process_context.fs
diff --git a/...te/isa_process_parameter_value_context.fs → ...te/isa_process_parameter_value_context.fs b/...te/isa_process_parameter_value_context.fs → ...te/isa_process_parameter_value_context.fs
diff --git a/.../context/ro-crate/isa_protocol_context.fs → ...n/context/rocrate/isa_protocol_context.fs b/.../context/ro-crate/isa_protocol_context.fs → ...n/context/rocrate/isa_protocol_context.fs
diff --git a/...o-crate/isa_protocol_parameter_context.fs → ...rocrate/isa_protocol_parameter_context.fs b/...o-crate/isa_protocol_parameter_context.fs → ...rocrate/isa_protocol_parameter_context.fs
diff --git a/...ntext/ro-crate/isa_publication_context.fs → ...ontext/rocrate/isa_publication_context.fs b/...ntext/ro-crate/isa_publication_context.fs → ...ontext/rocrate/isa_publication_context.fs
diff --git a/...on/context/ro-crate/isa_sample_context.fs → ...son/context/rocrate/isa_sample_context.fs b/...on/context/ro-crate/isa_sample_context.fs → ...son/context/rocrate/isa_sample_context.fs
diff --git a/...on/context/ro-crate/isa_source_context.fs → ...son/context/rocrate/isa_source_context.fs b/...on/context/ro-crate/isa_source_context.fs → ...son/context/rocrate/isa_source_context.fs
diff --git a/...son/context/ro-crate/isa_study_context.fs → ...Json/context/rocrate/isa_study_context.fs b/...son/context/ro-crate/isa_study_context.fs → ...Json/context/rocrate/isa_study_context.fs
diff --git a/....Json/context/ro-crate/rocrate_context.fs → ...A.Json/context/rocrate/rocrate_context.fs b/....Json/context/ro-crate/rocrate_context.fs → ...A.Json/context/rocrate/rocrate_context.fs
diff --git a/tests/ISA/ISA.Json.Tests/Json.Tests.fs b/tests/ISA/ISA.Json.Tests/Json.Tests.fs
@@ -1292,7 +1292,7 @@ let testInvestigationFile =
                 Publication.make
                     (Some "12345678")
                     (Some "11.1111/abcdef123456789")
-                    (Some "Lukas Weil, Other Gzúy")
+                    (Some "Lukas Weil, Other Gzuy") // (Some "Lukas Weil, Other Gzúy")
                     (Some "Fair is great")
                     (Some publicationStatus)
                     (Some [|comment|])
@@ -1708,7 +1708,7 @@ let testInvestigationFileLD =
                 Publication.make
                     (Some "12345678")
                     (Some "11.1111/abcdef123456789")
-                    (Some "Lukas Weil, Other Gzúy")
+                    (Some "Lukas Weil, Other Gzuy") // (Some "Lukas Weil, Other Gzúy")
                     (Some "Fair is great")
                     (Some publicationStatus)
                     (Some [|comment|])
@@ -2051,7 +2051,7 @@ let testInvestigationFileLD =
                 Publication.make
                     (Some "12345678")
                     (Some "11.1111/abcdef123456789")
-                    (Some "Lukas Weil, Other Gzúy")
+                    (Some "Lukas Weil, Other Gzuy") // (Some "Lukas Weil, Other Gzúy")
                     (Some "Fair is great")
                     (Some publicationStatus)
                     (Some [|comment|])