LeibnizDSMZ · juwitte · Feb 4, 2025 · Jan 15, 2025 · Jan 20, 2025 · Feb 4, 2025
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -2,26 +2,29 @@ name: main
 
 on:
   pull_request:
+  push:
     branches: [main]
 
 jobs:
   mac_win_test:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.13']
         os: [windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@v3
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install -r configs/dev/requirements.test.txt
+        pip install .
         pip install tox
     - name: tox test
       run: |
@@ -34,10 +37,10 @@ jobs:
       fail-fast: false
     runs-on: ubuntu-latest
     steps:
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v3
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.13'
     - name: Install dependencies
       run: |
         sudo mkdir -p $CU_HOME && sudo chown runner -R $CU_HOME
@@ -46,7 +49,7 @@ jobs:
         echo "$CU_HOME/$PY_DIR/bin" >> $GITHUB_PATH
         echo "$CU_HOME/$PY_DIR/shims" >> $GITHUB_PATH
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: lint and test

diff --git a/.github/workflows/mkdocs.yml b/.github/workflows/mkdocs.yml
@@ -21,10 +21,10 @@ jobs:
       CU_HOME: /home/custom
     runs-on: ubuntu-latest
     steps:
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v3
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.13'
     - name: Install dependencies
       run: |
         sudo mkdir -p $CU_HOME && sudo chown runner -R $CU_HOME
@@ -33,15 +33,15 @@ jobs:
         echo "$CU_HOME/$PY_DIR/bin" >> $GITHUB_PATH
         echo "$CU_HOME/$PY_DIR/shims" >> $GITHUB_PATH
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Setup Pages
-      uses: actions/configure-pages@v3
+      uses: actions/configure-pages@v5
     - name: Create documentation html
       run: |
         make docs
         make runDocs
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v1
+      uses: actions/upload-pages-artifact@v3
       with:
         path: ./public
   deploy:
@@ -53,4 +53,4 @@ jobs:
     steps:
     - name: Deploy to GitHub Pages
       id: deployment
-      uses: actions/deploy-pages@v2
+      uses: actions/deploy-pages@v4
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,13 @@
+## v0.2.0 (2025-02-04)
+
+### Feat
+
+- source now list of sourcestrings
+
+### Fix
+
+- solve "None" fields are not required
+
 ## v0.1.1 (2025-01-15)
 
 ### Fix

diff --git a/Makefile b/Makefile
@@ -23,8 +23,6 @@ setup:
 	$(POETRY) env remove --all
 	$(POETRY) config virtualenvs.in-project true
 	$(POETRY) env use `pyenv which python`
-	$(POETRY) self add poetry-plugin-export
-	$(POETRY) self add poetry-plugin-shell
 
 uninstall:
 	pyenv local $(PYV)

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![release: 0.1.1](https://img.shields.io/badge/rel-0.1.1-blue.svg?style=flat-square)](https://github.com/LeibnizDSMZ/microbial-data-standard)
+[![release: 0.2.0](https://img.shields.io/badge/rel-0.2.0-blue.svg?style=flat-square)](https://github.com/LeibnizDSMZ/microbial-data-standard)
 [![MIT LICENSE](https://img.shields.io/badge/License-MIT-brightgreen.svg?style=flat-square)](https://choosealicense.com/licenses/mit/)
 [![Documentation Status](https://img.shields.io/badge/docs-GitHub-blue.svg?style=flat-square)](https://LeibnizDSMZ.github.io/microbial-data-standard/)
 

diff --git a/docs/graph.md b/docs/graph.md
@@ -457,7 +457,7 @@ gamma
 }
 
 class `CultivationMedia`{
-name: string | null
+name: string
 url: string | null
 reagentUsed: string
 source: string
@@ -562,7 +562,7 @@ availability: boolean | null
 catalogUrl: string | null
 restrictionsOnUse: Restriction | null
 axenicCulture: boolean | null
-supplyForms: array | null
+supplyForms: array[SupplyForm]
 history: string | null
 depositionDate: string | null
 depositor: Person | null
@@ -576,6 +576,18 @@ Only for non-commercial purposes
 For commercial development a special agreement is requested
 }
 
+class `SupplyForm`{
+<<enumeration>>
+Agar
+Cryo
+Dry ice
+Liquid medium
+Lyo
+Oil
+Water
+DNA
+}
+
 class `OtherMedia`{
 url: string | null
 name: string | null
@@ -722,6 +734,7 @@ sources:
 `Collection` ..> `Identifier`
 `Collection` ..> `Address`
 `Collection` ..> `Restriction`
+`Collection` ..> `SupplyForm`
 `Collection` ..> `Person`
 `Microbe` ..> `OtherMedia`
 ```
diff --git a/docs/schema/05. typeStrain.md b/docs/schema/05. typeStrain.md
@@ -15,6 +15,6 @@ Type Strain  `Required`
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/06. taxon.md b/docs/schema/06. taxon.md
@@ -136,6 +136,6 @@ Same As
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/07. sample.md b/docs/schema/07. sample.md
@@ -137,6 +137,9 @@ Precision
 ## 07.5. sample.tags
 Isolation Source Tags  
 
+Description:
+> Isolation tag system, original used by BacDive  
+
 **array[object]**
 
 ---
@@ -162,6 +165,6 @@ Level 3
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/08. isolation.md b/docs/schema/08. isolation.md
@@ -69,7 +69,7 @@ Address
 
 ---
 ## 08.2.4.1. isolation.isolatedAt.address.addressCountry
-Country  `Required`
+Country  
 
 **string, null**
 
@@ -159,6 +159,6 @@ URL
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/09. legal.md b/docs/schema/09. legal.md
@@ -65,6 +65,6 @@ GMO Information
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/10. cellShape.md b/docs/schema/10. cellShape.md
@@ -15,6 +15,6 @@ Cell Shape  `Required`
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/11. oxygenRelation.md b/docs/schema/11. oxygenRelation.md
@@ -15,6 +15,6 @@ Oxygen Relation  `Required`
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/12. multiCellComplexForming.md b/docs/schema/12. multiCellComplexForming.md
@@ -15,6 +15,6 @@ Multi Cell Complex Forming  `Required`
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/13. cellSize.md b/docs/schema/13. cellSize.md
@@ -87,6 +87,6 @@ Enum:
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/14. motility.md b/docs/schema/14. motility.md
@@ -39,6 +39,6 @@ Gliding
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/15. colony.md b/docs/schema/15. colony.md
@@ -66,6 +66,6 @@ Enum:
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/16. sporeFormation.md b/docs/schema/16. sporeFormation.md
@@ -39,6 +39,6 @@ Spore Ejection
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/17. temperature.md b/docs/schema/17. temperature.md
@@ -28,10 +28,6 @@ Unit  `Required`
 
 **string**
 
-Enum:
-
-	C
-
 ---
 ## 17.5. temperature.tested
 Tests  
@@ -56,10 +52,6 @@ Unit  `Required`
 
 **string**
 
-Enum:
-
-	C
-
 ---
 ## 17.5.4. temperature.tested.growth
 Growth  `Required`
@@ -71,6 +63,6 @@ Growth  `Required`
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/18. pH.md b/docs/schema/18. pH.md
@@ -28,10 +28,6 @@ Unit  `Required`
 
 **string**
 
-Enum:
-
-	pH
-
 ---
 ## 18.5. pH.tested
 Tests  
@@ -56,10 +52,6 @@ Unit  `Required`
 
 **string**
 
-Enum:
-
-	pH
-
 ---
 ## 18.5.4. pH.tested.growth
 Growth  `Required`
@@ -71,6 +63,6 @@ Growth  `Required`
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/19. identifier.md b/docs/schema/19. identifier.md
@@ -33,6 +33,6 @@ URL
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/20. connectedPersons.md b/docs/schema/20. connectedPersons.md
@@ -60,6 +60,6 @@ Enum:
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/21. pathogenicity.md b/docs/schema/21. pathogenicity.md
@@ -65,6 +65,6 @@ Classification
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**
diff --git a/docs/schema/22. bioSafety.md b/docs/schema/22. bioSafety.md
@@ -27,6 +27,6 @@ URL
 Source  `Required`
 
 Description:
-> JSON path to source object  
+> List of JSON paths to source object  
 
-**string**
+**array[string]**