Improve the docs

Author: mr-c

cwltool/cwlprov/ro.py

@@ -402,6 +402,7 @@ def guess_mediatype(
         return aggregates
 
     def add_uri(self, uri: str, timestamp: Optional[datetime.datetime] = None) -> Aggregate:
+        """Add the given URI to this RO."""
         self.self_check()
         aggr: Aggregate = {"uri": uri}
         aggr["createdOn"], aggr["createdBy"] = self._self_made(timestamp=timestamp)

cwltool/cwlrdf.py

@@ -1,3 +1,5 @@
+"""RDF output."""
+
 from typing import IO, Any
 
 from rdflib import Graph

cwltool/factory.py

@@ -27,6 +27,7 @@ def __init__(self, t: Process, factory: "Factory") -> None:
 
     def __call__(self, **kwargs):
         # type: (**Any) -> Union[str, Optional[CWLObjectType]]
+        """Invoke the tool."""
         runtime_context = self.factory.runtime_context.copy()
         runtime_context.basedir = os.getcwd()
         out, status = self.factory.executor(self.t, kwargs, runtime_context)

cwltool/job.py

@@ -100,6 +100,7 @@ def relink_initialworkdir(
 
 
 def neverquote(string: str, pos: int = 0, endpos: int = 0) -> Optional[Match[str]]:
+    """No-op."""
     return None
 
 

cwltool/resolver.py

@@ -11,6 +11,7 @@
 
 
 def resolve_local(document_loader: Optional[Loader], uri: str) -> Optional[str]:
+    """Use the local resolver to find the target of the URI."""
     pathpart, frag = urllib.parse.urldefrag(uri)
 
     try:
@@ -41,6 +42,7 @@ def resolve_local(document_loader: Optional[Loader], uri: str) -> Optional[str]:
 
 
 def tool_resolver(document_loader: Loader, uri: str) -> Optional[str]:
+    """Try both the local resolver and the GA4GH TRS resolver, in that order."""
     for r in [resolve_local, resolve_ga4gh_tool]:
         ret = r(document_loader, uri)
         if ret is not None:
@@ -63,6 +65,7 @@ def tool_resolver(document_loader: Loader, uri: str) -> Optional[str]:
 
 
 def resolve_ga4gh_tool(document_loader: Loader, uri: str) -> Optional[str]:
+    """Use the GA4GH TRS API to resolve a tool reference."""
     path, version = uri.partition(":")[::2]
     if not version:
         version = "latest"

cwltool/stdfsaccess.py

@@ -55,6 +55,7 @@ def listdir(self, fn: str) -> list[str]:
         return [abspath(urllib.parse.quote(entry), fn) for entry in os.listdir(self._abs(fn))]
 
     def join(self, path, *paths):  # type: (str, *str) -> str
+        """Join one or more path segments intelligently."""
         return os.path.join(path, *paths)
 
     def realpath(self, path: str) -> str: