Comments (2)
@MordorianGuy you are right that data
or alignment
makes more sense -- however, for reasons of backward compatibility, it is not easy to change this. All BEAST v2.7.x compatible XML should still run on BEAST v2.7.y for y>x. There are a few more inconsistencies in Input names (e.g. start as capital in IsLabeledNewick
in TreeParser
, and these should be the same names: BeautiSubTemplate.suppressInputs
BeautiConfig.suppressPlugins
)
It can be achieved by adding an extra Input and deprecating the old one, or creating a new type of input that is known by more than one name (taxa
and data
for example), or perhaps some other mechanism for redirecting the Input values to the original Input. Not sure what the optimal solution is to remain both backward compatible and allow introduction of input name changes.
from beast2.
@MordorianGuy you are right that
data
oralignment
makes more sense -- however, for reasons of backward compatibility, it is not easy to change this. All BEAST v2.7.x compatible XML should still run on BEAST v2.7.y for y>x. There are a few more inconsistencies in Input names (e.g. start as capital inIsLabeledNewick
inTreeParser
, and these should be the same names:BeautiSubTemplate.suppressInputs
BeautiConfig.suppressPlugins
)It can be achieved by adding an extra Input and deprecating the old one, or creating a new type of input that is known by more than one name (
taxa
anddata
for example), or perhaps some other mechanism for redirecting the Input values to the original Input. Not sure what the optimal solution is to remain both backward compatible and allow introduction of input name changes.
Thank you for your answer!
Yes, you are right: the backward compatibility is hard. I have thought more about something like regex switches between versions applying to parsed XML based on the version attribute of the beast tag. If we definitely know what we changed between specific versions, we may apply these changes consequently to adjust an old XML to new standards. At least if we talk about simple renaming.
from beast2.
Related Issues (20)
- Transform for interval, lower and upper bounds missing
- Generalization of root and tip distributions as RootDistribution and TipDistribution
- Prep for v2.7.5 release
- RPNCalculator argnames input
- About BEAST2 run error HOT 4
- beauti doesn't format html in package descriptions.
- Tree.printTranslate not robust HOT 1
- BEAUti does not set a specified Clock.rate of `ClusterTree`. HOT 5
- Input setStringValue for non-numerical list inputs
- BactrianUpDownOperator modifies the wrong index when elementWise is true HOT 1
- Warning: Duplicate cpuset controllers detected HOT 7
- Running into errors when following "WRITING A BEAST 2.7 PACKAGE" guide HOT 4
- AdaptableOperatorSampler should have a try catch around calling the tree metrix
- Parameter does not restore properly after dimension change
- Prep for v2.7.6 release
- BEAST2: fatal error has been detected by the Java Runtime Environment HOT 3
- Robustify package manager
- How can I find out number of patterns and number of partitions from my input file without running Beast2? HOT 6
- java.lang.Error: randomChoiceUnnormalized falls through -- negative components in input distribution? HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from beast2.