Update MESSAGEix-Transport usage docs; use Windows-friendly file name…

…s in tests (iiasa#158)

- Correct name format of xlsx file in test_report_bare
  Remove colon (:) from the name of the reporting file that was leading the test to fail in Windows in test_report_bare
- Correct typo in shell usage example
- Improve documentation for building a MESSAGEix-Transport model
- Expand transport usage docs
- Squash warnings in docs build

Co-authored-by: Paul Natsuo Kishimoto <mail@paul.kishimoto.name>

message_ix_models/report/util.py

@@ -61,7 +61,7 @@
 
 
 def collapse(df, var_name, var=[], region=[], replace_common=True):
-    """Callback for the `collapse argument to :meth:`~.Reporter.convert_pyam.
+    """Callback for the `collapse` argument to :meth:`~.Reporter.convert_pyam`.
 
     The dimensions listed in the `var` and `region` arguments are automatically
     dropped from the returned :class:`pyam.IamDataFrame`.