Merge pull request #212 from mvdbeek/explicit_none

Use None default value where items are optional

Author: mvdbeek

src/ephemeris/_config_models.py

@@ -18,13 +18,13 @@
 class RepositoryInstallTarget(BaseModel):
     name: str
     owner: str
-    tool_shed_url: Optional[str]
-    tool_panel_section_id: Optional[str]
-    tool_panel_section_label: Optional[str]
-    revisions: Optional[List[str]]
-    install_tool_dependencies: Optional[bool]
-    install_repository_dependencies: Optional[bool]
-    install_resolver_dependencies: Optional[bool]
+    tool_shed_url: Optional[str] = None
+    tool_panel_section_id: Optional[str] = None
+    tool_panel_section_label: Optional[str] = None
+    revisions: Optional[List[str]] = None
+    install_tool_dependencies: Optional[bool] = None
+    install_repository_dependencies: Optional[bool] = None
+    install_resolver_dependencies: Optional[bool] = None
 
 
 class RepositoryInstallTargets(BaseModel):
@@ -46,22 +46,26 @@ class DataManagers(BaseModel, extra=Extra.forbid):
 
 class Genome(BaseModel):
     id: str  # The unique id of the data in Galaxy
-    description: str  # The description of the data, including its taxonomy, version and date
-    dbkey: Optional[str]
-    source: Optional[str]  # The source of the data. Can be: 'ucsc', an NCBI accession number or a URL to a fasta file.
+    description: Optional[str] = None  # The description of the data, including its taxonomy, version and date
+    dbkey: Optional[str] = None
+    source: Optional[str] = (
+        None  # The source of the data. Can be: 'ucsc', an NCBI accession number or a URL to a fasta file.
+    )
 
     # The following fields are currently purely for human consumption and unused by
     # IDC infrastructure.
-    doi: Optional[str]  # Any DOI associated with the data
-    blob: Optional[str]  # A blob for any other pertinent information
-    checksum: Optional[str]  # A SHA256 checksum of the original
-    version: Optional[str]  # Any version information associated with the data
+    doi: Optional[str] = None  # Any DOI associated with the data
+    blob: Optional[str] = None  # A blob for any other pertinent information
+    checksum: Optional[str] = None  # A SHA256 checksum of the original
+    version: Optional[str] = None  # Any version information associated with the data
 
     # Description of actions (data managers) to run on target genome.
     indexers: Optional[
         List[str]
     ]  # indexers to run - keyed on repository name - see data_managers.yml for how to resolve these to tools
-    skiplist: Optional[List[str]]  # unimplemented: but if we implement classes of indexers, these will be ones to skip
+    skiplist: Optional[List[str]] = (
+        None  # unimplemented: but if we implement classes of indexers, these will be ones to skip
+    )
 
 
 class Genomes(BaseModel):