Changes between Version 4 and Version 5 of Dev2021-9-2

Timestamp:

Sep 2, 2021, 3:21:15 PM (4 years ago)

Author:

Tom Goddard

Comment:

--

Dev2021-9-2

@@ -29 +29 @@
   - Apache hard to configure https for multiple sites.
 
+* Sphinx and doc strings
+  - Zach suggests we use the Sphinx napolean extension included with Sphinx instead of numpydoc.
+  - Napolean handles numpy and google doc string formats.
+  - Zach will test it and show us good examples of how to format our doc strings.
+
+* Python type hints
+  - Discussed the advantages and disadvantages of Python type hints in function arguments and class attributes.
+  - Eric points out ChimeraX plugin developers may find these hints confusing.
+  - Greg points out speed optimizers for Python are trying to use type hints.  Guido has come out of retirement trying to increase CPython speed 2 fold.
+  - Zach says type hints produce runtime error when wrong argument type passed that helps him debug code faster.
+  - Zach suggests using a Sphinx extension so the type hints do not appear in function signatures in the documentation.
+  - Decided that each developer can choose whether to use type hints.
+  - Greg thinks might be possible that ChimeraX command registration could introspect function argument type hints instead of declaring the argument types in the registration call.
+
+* Blast threading
+  - Zach asks how to avoid blocking after BLAST rest returns results while code is fetching files containing results.  Can QThread be used?
+  - Could use a Task.
+  - Current blast gui in ChimeraX 1.2.5 blocks for 40 seconds on  4v6x chain A (900 hits) while loading results.
+  - Suggest Zach complete new Qt blast gui before worrying about optimization.
+
+* mmCIF saving error
+  - Greg says user tried to save NMR ensemble where chain names were changed, gave traceback.
+  - Will put in error checking.
+  - mmCIF save tries to extract info from chimerax data structures that can be inconsistent and needs checking for compatibility with mmcif requirements.
+
+* Roadmap for 1.3 release
+  - Everyone update the 1.3 roadmap moving stuff that won't make it into 1.3 to the 1.4 milestone.
+
 = Action Items =