Closed xrotwang closed 5 years ago
What remains to do:
Merging #247 into master will not change coverage. The diff coverage is
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beastling/__main__.py | 0% <ø> (ø) |
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beastling/models/covarion.py | 0% <0%> (ø) |
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beastling/extractor.py | 0% <0%> (ø) |
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beastling/util/misc.py | 0% <0%> (ø) |
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beastling/models/basemodel.py | 0% <0%> (ø) |
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beastling/report.py | 0% <0%> (ø) |
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beastling/treepriors/base.py | 0% <0%> (ø) |
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beastling/clocks/prior.py | 0% <0%> (ø) |
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beastling/models/geo.py | 0% <0%> (ø) |
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beastling/beastxml.py | 0% <0%> (ø) |
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@lmaurits @Anaphory I just pushed a commit replacing the messages
mechanism with standard python logging. Let me know if you'd want this to be reverted. Using logging feels a lot more "right" to me, though - in particular because we had this ad-hoc re-invention of log levels as part of the message before.
See https://github.com/lmaurits/BEASTling/pull/247/commits/0beec0312075176ba2c09a69fbef730b7663c49a#diff-4d1ff12693ff7665889a62c693b937cd for the new logging functionality. Usage is simple:
from beastling.util import log
...
log.info('msg', model=...)
log.dependency('function', 'package')
...
Just from a first glance without checks and tests yet: Sweet!
How will we deal with models? It feels like there should be some sub-classes involved, do you already know how to do that?
@Anaphory I'd go for the geo sections next, and then cook something up for models.
Another "next step" I see here is adding write support to Section
- basically the inverse of from_config
. This would allow us to also embed a valid BEASTling config into the BEAST XML when it was created programmatically.
Options of the core config sections
admin
,mcmc
andlanguages
are now accessed as attributes of instances of the respectivesections.Section
subclass and not as direct attributes ofConfiguration
.This
Configuration
Closes #243